Last updated: 2025-07-22
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Knit directory: phasing_clean/
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Here in this document we present figures, tables, and statistics for the phasing evaluation on the autosomes. This sample consists of 602 individuals phased using a reference panel of unrelated individuals from the 1000 genomes project. The phasing results are compared to a pedigree-adjusted phased genome for each sample.
library(tidyverse)
library(pander)
library(reactable)
library(yaml)
library(gtsummary)
library(grid)
library(gridExtra)
config_obj <- yaml::read_yaml("_config.yaml")
cbPalette <- c("#999999", "#E69F00", "#56B4E9", "#009E73", "#F0E442", "#0072B2", "#D55E00", "#CC79A7")
df_subj <- read_csv("data/1kgp/subject_info.csv")
ped_df <- read_table("data/1kgp/1kGP.3202_samples.pedigree_info.txt")
child_ids <- ped_df %>% filter(fatherID != "0" & motherID != "0") %>% pull(sampleID)
unrel_ids <- scan("data/1kgp/unrelated_subjects.txt", what = character())
df_subj_rel <- df_subj %>%
filter(SAMPLE_NAME %in% child_ids)
df_subj_rel$id2 <- 1:602
df_subj_unrel <- df_subj %>%
filter(SAMPLE_NAME %in% unrel_ids)
df_switch_trio <- vector(mode = "list", length = 22)
for(i in 1:22){
df_switch_trio[[i]] <- read_csv(paste0(config_obj$base_dir, "/output/trio_phase_", i, "/switch_errors/summary.csv"),
show_col_types = FALSE)
}
And let’s also load the results from when we phase without the triple heterozygous positions:
df_switch_trio_noth <- read_csv("output/all_noTH.csv", show_col_types = F)
# het dfs
df_het <- vector(mode = "list", length = 22)
for(i in 1:22){
df_het[[i]] <- read_tsv(paste0(config_obj$base_dir, "/output/trio_phase_", i, "/no_th/het_pos_count.tsv"),
col_names = c("id", "n_het"),
show_col_types = FALSE)
}
df_decode <- vector(mode = "list", length = 22)
for(i in 1:22){
df_decode[[i]] <- read_tsv(paste0("data/decode/chr", i, "_recomb.bed"), col_names = c("chr", "start", "end", "cM_MB"), show_col_types = FALSE)
}
We’ll also pull in the results on chromosome X for the synthetic diploids to allow for comparisons of rates between 15 and X.
sd_pair_info_df <- read_delim("data/sample_pairs.csv", col_names = c("POP", "ID1", "ID2"))
Rows: 1000 Columns: 3
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (3): POP, ID1, ID2
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
sd_pair_info_df <- left_join(sd_pair_info_df, df_subj, by = c("ID1"="SAMPLE_NAME")) %>%
rename(SP = SUPER) %>%
select(-POPULATION)
df_switch_x <- read_csv(paste0(config_obj$base_dir,"/output/switch_errors/switch_errors/summary.csv"))
Rows: 1000 Columns: 45
── Column specification ────────────────────────────────────────────────────────
Delimiter: ","
chr (2): pop, subpop
dbl (43): pair_id, n_switch_eagle, n_switch_beagle, n_switch_shapeit, n_flip...
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
df_het_x <- read_tsv(paste0(config_obj$base_dir, "/output/switch_errors/het_pos_count.tsv"), col_names = c("id", "n_het"))
Rows: 1000 Columns: 2
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
dbl (2): id, n_het
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
n_var_site_x <- 1722954
df_het_x$frac_het <- df_het_x$n_het / n_var_site_x
sd_pair_info_df$n_het <-df_het_x$n_het
sd_pair_info_df$frac_het <-df_het_x$frac_het
df_decode_x <- read_tsv("data/decode/chrX_recomb.bed", col_names = c("chr", "start", "end", "cM_MB"))
Rows: 23976 Columns: 4
── Column specification ────────────────────────────────────────────────────────
Delimiter: "\t"
chr (1): chr
dbl (3): start, end, cM_MB
ℹ Use `spec()` to retrieve the full column specification for this data.
ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.
The 1000 Genomes collection of 3,202 genomes is sampled from 26 different populations, each belonging to 1 of 5 distinct super-populations (AFR, AMR, EAS, EUR, SAS). All 26 populations are represented in the 2,504 1kGP phase 3 subjects, but not all are present in the 602 trios sequenced by the New York Genome Center:
df_subj %>%
group_by(SUPER, POPULATION) %>%
summarize(N = n()) %>%
reactable(
groupBy = c("SUPER"),
columns = list(
N = colDef(aggregate = "sum")),
bordered = TRUE,
defaultExpanded = TRUE)
`summarise()` has grouped output by 'SUPER'. You can override using the
`.groups` argument.
df_subj_rel %>%
group_by(SUPER, POPULATION) %>%
summarize(N = n()) %>%
reactable(
groupBy = c("SUPER"),
columns = list(
N = colDef(aggregate = "sum")),
bordered = TRUE,
defaultExpanded = TRUE)
`summarise()` has grouped output by 'SUPER'. You can override using the
`.groups` argument.
df_subj_unrel %>%
group_by(SUPER, POPULATION) %>%
summarize(N = n()) %>%
reactable(
groupBy = c("SUPER"),
columns = list(
N = colDef(aggregate = "sum")),
bordered = TRUE,
defaultExpanded = TRUE)
`summarise()` has grouped output by 'SUPER'. You can override using the
`.groups` argument.
For completeness, we also tabulate other summary information about the 602 trios (which is just sex; 1 - male, 2 - female):
df_subj_rel %>%
group_by(sex) %>%
summarize(N = n()) %>%
reactable(
groupBy = c("sex"),
columns = list(
N = colDef(aggregate = "sum")),
bordered = TRUE,
defaultExpanded = TRUE)
df_subj_unrel %>%
group_by(sex) %>%
summarize(N = n()) %>%
reactable(
groupBy = c("sex"),
columns = list(
N = colDef(aggregate = "sum")),
bordered = TRUE,
defaultExpanded = TRUE)
First let’s get an overall error rate across all 22 autosomes based on our re-phasing of the trio probands:
df_total <- df_switch_trio[[1]] %>%
mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
mutate(chrom = 1)
df_total_noth <- df_switch_trio_noth %>%
mutate(Eagle = (n_switch_e + n_flip_e) / n_het,
Beagle = (n_switch_b + n_flip_b) / n_het,
SHAPEIT = (n_switch_s + n_flip_s) / n_het) %>%
select(Eagle, Beagle, SHAPEIT, sample, chrom)
df_total_noth <- df_total_noth %>%
left_join({df_subj_rel %>% select(id2, SUPER)}, by = c("sample" = "id2")) %>%
rename(pair_id = sample) %>%
select(Eagle, Beagle, SHAPEIT, SUPER, pair_id, chrom)
for(i in 2:22){
df_total <- bind_rows(df_total,
{
df_switch_trio[[i]] %>%
mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
mutate(chrom = i)
})
}
df_total <- df_total %>%
bind_rows({df_switch_x %>%
mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
rename(SUPER = pop) %>%
select(Eagle, Beagle, SHAPEIT, SUPER) %>%
mutate(pair_id = 603:1602, chrom = 23)})
df_total_noth <- df_total_noth %>%
bind_rows({df_switch_x %>%
mutate(Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
rename(SUPER = pop) %>%
select(Eagle, Beagle, SHAPEIT, SUPER) %>%
mutate(pair_id = 603:1602, chrom = 23)})
df_total %>%
group_by(chrom) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
knitr::kable()
| chrom | Beagle | Eagle | SHAPEIT |
|---|---|---|---|
| 1 | 0.0067395 | 0.0067223 | 0.0071348 |
| 2 | 0.0067182 | 0.0066709 | 0.0071241 |
| 3 | 0.0062862 | 0.0062368 | 0.0066700 |
| 4 | 0.0058272 | 0.0058086 | 0.0061830 |
| 5 | 0.0062772 | 0.0062116 | 0.0066640 |
| 6 | 0.0056205 | 0.0056106 | 0.0059695 |
| 7 | 0.0066444 | 0.0066400 | 0.0070178 |
| 8 | 0.0016721 | 0.0022869 | 0.0017815 |
| 9 | 0.0079744 | 0.0079202 | 0.0083190 |
| 10 | 0.0064289 | 0.0064593 | 0.0068026 |
| 11 | 0.0063130 | 0.0062888 | 0.0066795 |
| 12 | 0.0064549 | 0.0064011 | 0.0068462 |
| 13 | 0.0062073 | 0.0061843 | 0.0065682 |
| 14 | 0.0069985 | 0.0070401 | 0.0074116 |
| 15 | 0.0080919 | 0.0081443 | 0.0085070 |
| 16 | 0.0080883 | 0.0081102 | 0.0085211 |
| 17 | 0.0082995 | 0.0083780 | 0.0086566 |
| 18 | 0.0066549 | 0.0066279 | 0.0070294 |
| 19 | 0.0077351 | 0.0078323 | 0.0080561 |
| 20 | 0.0080259 | 0.0080467 | 0.0083414 |
| 21 | 0.0086549 | 0.0088189 | 0.0090797 |
| 22 | 0.0098210 | 0.0100373 | 0.0101722 |
| 23 | 0.0030794 | 0.0036645 | 0.0031251 |
df_total %>%
group_by(chrom, SUPER) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
knitr::kable()
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.
| chrom | SUPER | Beagle | Eagle | SHAPEIT |
|---|---|---|---|---|
| 1 | AFR | 0.0055470 | 0.0052014 | 0.0058600 |
| 1 | AMR | 0.0064375 | 0.0065297 | 0.0068945 |
| 1 | EAS | 0.0092799 | 0.0096876 | 0.0097752 |
| 1 | EUR | 0.0062678 | 0.0063948 | 0.0065600 |
| 1 | SAS | 0.0084880 | 0.0085297 | 0.0090237 |
| 2 | AFR | 0.0054907 | 0.0051472 | 0.0058282 |
| 2 | AMR | 0.0066014 | 0.0066504 | 0.0070537 |
| 2 | EAS | 0.0092474 | 0.0095998 | 0.0098008 |
| 2 | EUR | 0.0060698 | 0.0061718 | 0.0063560 |
| 2 | SAS | 0.0084829 | 0.0084545 | 0.0090015 |
| 3 | AFR | 0.0051191 | 0.0047501 | 0.0054396 |
| 3 | AMR | 0.0060628 | 0.0061345 | 0.0065287 |
| 3 | EAS | 0.0087136 | 0.0090203 | 0.0091782 |
| 3 | EUR | 0.0058531 | 0.0059451 | 0.0060974 |
| 3 | SAS | 0.0078949 | 0.0079269 | 0.0084038 |
| 4 | AFR | 0.0047064 | 0.0043872 | 0.0049933 |
| 4 | AMR | 0.0058144 | 0.0058702 | 0.0062470 |
| 4 | EAS | 0.0078453 | 0.0082126 | 0.0082989 |
| 4 | EUR | 0.0053370 | 0.0054733 | 0.0055894 |
| 4 | SAS | 0.0074061 | 0.0074566 | 0.0078482 |
| 5 | AFR | 0.0051628 | 0.0047968 | 0.0055004 |
| 5 | AMR | 0.0060247 | 0.0060731 | 0.0064754 |
| 5 | EAS | 0.0086690 | 0.0089300 | 0.0091428 |
| 5 | EUR | 0.0057598 | 0.0058361 | 0.0060024 |
| 5 | SAS | 0.0079450 | 0.0079505 | 0.0084528 |
| 6 | AFR | 0.0046691 | 0.0044083 | 0.0049870 |
| 6 | AMR | 0.0054834 | 0.0055737 | 0.0058509 |
| 6 | EAS | 0.0076252 | 0.0079459 | 0.0080756 |
| 6 | EUR | 0.0050195 | 0.0050966 | 0.0052602 |
| 6 | SAS | 0.0071493 | 0.0071820 | 0.0075932 |
| 7 | AFR | 0.0056451 | 0.0053659 | 0.0059259 |
| 7 | AMR | 0.0063283 | 0.0064342 | 0.0068119 |
| 7 | EAS | 0.0089896 | 0.0092754 | 0.0094416 |
| 7 | EUR | 0.0060694 | 0.0061896 | 0.0063094 |
| 7 | SAS | 0.0082539 | 0.0083194 | 0.0087699 |
| 8 | AFR | 0.0017555 | 0.0020756 | 0.0018302 |
| 8 | AMR | 0.0023261 | 0.0029894 | 0.0024296 |
| 8 | EAS | 0.0007489 | 0.0019593 | 0.0007036 |
| 8 | EUR | 0.0011225 | 0.0018524 | 0.0012282 |
| 8 | SAS | 0.0018944 | 0.0024787 | 0.0022310 |
| 9 | AFR | 0.0068396 | 0.0064942 | 0.0071230 |
| 9 | AMR | 0.0075185 | 0.0075597 | 0.0079218 |
| 9 | EAS | 0.0107378 | 0.0110860 | 0.0111549 |
| 9 | EUR | 0.0074135 | 0.0075191 | 0.0076602 |
| 9 | SAS | 0.0097581 | 0.0096966 | 0.0102146 |
| 10 | AFR | 0.0053702 | 0.0051045 | 0.0056988 |
| 10 | AMR | 0.0061843 | 0.0063284 | 0.0065907 |
| 10 | EAS | 0.0086799 | 0.0090581 | 0.0091298 |
| 10 | EUR | 0.0058815 | 0.0060049 | 0.0061312 |
| 10 | SAS | 0.0081091 | 0.0082448 | 0.0086279 |
| 11 | AFR | 0.0051038 | 0.0047643 | 0.0054421 |
| 11 | AMR | 0.0061504 | 0.0062567 | 0.0065811 |
| 11 | EAS | 0.0087048 | 0.0089563 | 0.0091293 |
| 11 | EUR | 0.0057273 | 0.0058646 | 0.0059475 |
| 11 | SAS | 0.0081458 | 0.0082203 | 0.0086106 |
| 12 | AFR | 0.0052336 | 0.0048435 | 0.0055285 |
| 12 | AMR | 0.0061647 | 0.0062722 | 0.0066160 |
| 12 | EAS | 0.0088507 | 0.0091833 | 0.0092980 |
| 12 | EUR | 0.0058835 | 0.0059865 | 0.0061495 |
| 12 | SAS | 0.0085005 | 0.0084572 | 0.0091331 |
| 13 | AFR | 0.0051338 | 0.0047588 | 0.0054669 |
| 13 | AMR | 0.0058467 | 0.0059489 | 0.0062847 |
| 13 | EAS | 0.0086166 | 0.0089850 | 0.0089645 |
| 13 | EUR | 0.0056813 | 0.0058049 | 0.0059074 |
| 13 | SAS | 0.0079485 | 0.0080400 | 0.0084311 |
| 14 | AFR | 0.0058491 | 0.0055279 | 0.0061819 |
| 14 | AMR | 0.0069236 | 0.0070836 | 0.0073920 |
| 14 | EAS | 0.0092338 | 0.0097126 | 0.0097585 |
| 14 | EUR | 0.0063719 | 0.0065804 | 0.0066770 |
| 14 | SAS | 0.0087328 | 0.0088611 | 0.0092879 |
| 15 | AFR | 0.0069205 | 0.0067038 | 0.0072805 |
| 15 | AMR | 0.0075491 | 0.0076851 | 0.0080371 |
| 15 | EAS | 0.0107938 | 0.0112109 | 0.0112988 |
| 15 | EUR | 0.0075873 | 0.0077744 | 0.0078511 |
| 15 | SAS | 0.0100833 | 0.0101590 | 0.0106255 |
| 16 | AFR | 0.0067101 | 0.0064605 | 0.0070518 |
| 16 | AMR | 0.0077841 | 0.0078624 | 0.0082867 |
| 16 | EAS | 0.0110409 | 0.0114166 | 0.0115555 |
| 16 | EUR | 0.0074827 | 0.0076739 | 0.0078211 |
| 16 | SAS | 0.0100990 | 0.0101592 | 0.0106840 |
| 17 | AFR | 0.0070385 | 0.0068052 | 0.0073412 |
| 17 | AMR | 0.0078579 | 0.0080042 | 0.0082180 |
| 17 | EAS | 0.0114246 | 0.0118422 | 0.0119096 |
| 17 | EUR | 0.0075552 | 0.0077852 | 0.0078145 |
| 17 | SAS | 0.0102826 | 0.0105113 | 0.0107783 |
| 18 | AFR | 0.0053748 | 0.0050216 | 0.0056865 |
| 18 | AMR | 0.0064686 | 0.0065122 | 0.0068916 |
| 18 | EAS | 0.0092433 | 0.0096255 | 0.0096967 |
| 18 | EUR | 0.0061722 | 0.0063152 | 0.0063982 |
| 18 | SAS | 0.0083972 | 0.0084671 | 0.0089623 |
| 19 | AFR | 0.0065154 | 0.0064078 | 0.0067781 |
| 19 | AMR | 0.0073732 | 0.0075864 | 0.0077798 |
| 19 | EAS | 0.0107155 | 0.0110315 | 0.0110440 |
| 19 | EUR | 0.0070417 | 0.0072541 | 0.0072739 |
| 19 | SAS | 0.0095512 | 0.0096150 | 0.0099775 |
| 20 | AFR | 0.0064594 | 0.0062060 | 0.0066644 |
| 20 | AMR | 0.0078739 | 0.0079705 | 0.0082688 |
| 20 | EAS | 0.0114298 | 0.0117419 | 0.0118613 |
| 20 | EUR | 0.0072520 | 0.0074422 | 0.0075192 |
| 20 | SAS | 0.0100663 | 0.0101533 | 0.0104775 |
| 21 | AFR | 0.0079544 | 0.0078804 | 0.0083141 |
| 21 | AMR | 0.0082498 | 0.0085883 | 0.0088090 |
| 21 | EAS | 0.0106827 | 0.0110631 | 0.0110567 |
| 21 | EUR | 0.0079347 | 0.0081427 | 0.0082329 |
| 21 | SAS | 0.0101535 | 0.0103601 | 0.0107176 |
| 22 | AFR | 0.0087059 | 0.0086329 | 0.0089909 |
| 22 | AMR | 0.0094276 | 0.0097295 | 0.0097832 |
| 22 | EAS | 0.0126112 | 0.0132342 | 0.0130122 |
| 22 | EUR | 0.0090470 | 0.0093067 | 0.0093290 |
| 22 | SAS | 0.0117030 | 0.0120662 | 0.0122487 |
| 23 | AFR | 0.0018961 | 0.0023549 | 0.0019652 |
| 23 | AMR | 0.0023216 | 0.0027562 | 0.0024143 |
| 23 | EAS | 0.0047907 | 0.0056040 | 0.0047650 |
| 23 | EUR | 0.0027532 | 0.0032940 | 0.0028181 |
| 23 | SAS | 0.0036354 | 0.0043134 | 0.0036627 |
df_total %>%
group_by(chrom) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
geom_point(size=3) +
theme_bw() +
xlab("Chromosome") +
ylab("Error Rate") +
labs(colour = "Method", shape = "Method") +
scale_colour_brewer(palette = "Set2") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
scale_x_continuous("Chromosome", labels = as.character(unique(df_total$chrom)), breaks = unique(df_total$chrom))

df_total %>%
group_by(chrom, SUPER) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
geom_point(size=2) +
theme_bw() +
ylab("Error Rate") +
xlab("Chromosome") +
labs(colour = "Population", shape = "Method") +
scale_colour_brewer(palette = "Set1")
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

df_total_noth %>%
group_by(chrom) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
knitr::kable()
| chrom | Beagle | Eagle | SHAPEIT |
|---|---|---|---|
| 1 | 0.0076521 | 0.0074991 | 0.0081145 |
| 2 | 0.0076647 | 0.0074667 | 0.0081643 |
| 3 | 0.0071878 | 0.0070196 | 0.0076684 |
| 4 | 0.0067061 | 0.0065728 | 0.0071506 |
| 5 | 0.0071902 | 0.0070086 | 0.0076810 |
| 6 | 0.0064784 | 0.0063175 | 0.0068826 |
| 7 | 0.0074391 | 0.0072982 | 0.0078961 |
| 8 | 0.0072741 | 0.0071112 | 0.0077785 |
| 9 | 0.0087028 | 0.0085344 | 0.0091643 |
| 10 | 0.0073034 | 0.0071957 | 0.0077402 |
| 11 | 0.0072545 | 0.0071127 | 0.0076998 |
| 12 | 0.0073676 | 0.0071869 | 0.0078629 |
| 13 | 0.0070782 | 0.0069520 | 0.0075517 |
| 14 | 0.0078292 | 0.0077546 | 0.0083515 |
| 15 | 0.0088513 | 0.0087992 | 0.0093716 |
| 16 | 0.0090042 | 0.0088870 | 0.0095468 |
| 17 | 0.0091358 | 0.0091251 | 0.0096319 |
| 18 | 0.0075749 | 0.0074640 | 0.0080646 |
| 19 | 0.0086534 | 0.0085857 | 0.0090404 |
| 20 | 0.0088541 | 0.0088080 | 0.0092697 |
| 21 | 0.0092530 | 0.0092396 | 0.0097647 |
| 22 | 0.0104660 | 0.0105487 | 0.0108801 |
| 23 | 0.0030794 | 0.0036645 | 0.0031251 |
df_total_noth %>%
group_by(chrom, SUPER) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
knitr::kable()
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.
| chrom | SUPER | Beagle | Eagle | SHAPEIT |
|---|---|---|---|---|
| 1 | AFR | 0.0061541 | 0.0056486 | 0.0065314 |
| 1 | AMR | 0.0073666 | 0.0073292 | 0.0079129 |
| 1 | EAS | 0.0106916 | 0.0109163 | 0.0112412 |
| 1 | EUR | 0.0071962 | 0.0072442 | 0.0075011 |
| 1 | SAS | 0.0096538 | 0.0095749 | 0.0103064 |
| 2 | AFR | 0.0061388 | 0.0056225 | 0.0065608 |
| 2 | AMR | 0.0075898 | 0.0075022 | 0.0081132 |
| 2 | EAS | 0.0107179 | 0.0108905 | 0.0113975 |
| 2 | EUR | 0.0069836 | 0.0069560 | 0.0073585 |
| 2 | SAS | 0.0096647 | 0.0095134 | 0.0103140 |
| 3 | AFR | 0.0057432 | 0.0052412 | 0.0061616 |
| 3 | AMR | 0.0070168 | 0.0069471 | 0.0075380 |
| 3 | EAS | 0.0100329 | 0.0102511 | 0.0106030 |
| 3 | EUR | 0.0067507 | 0.0067821 | 0.0070954 |
| 3 | SAS | 0.0090197 | 0.0089031 | 0.0096771 |
| 4 | AFR | 0.0053117 | 0.0048314 | 0.0056544 |
| 4 | AMR | 0.0067435 | 0.0067364 | 0.0072623 |
| 4 | EAS | 0.0091007 | 0.0094034 | 0.0097654 |
| 4 | EUR | 0.0062322 | 0.0062823 | 0.0065560 |
| 4 | SAS | 0.0085118 | 0.0083951 | 0.0090426 |
| 5 | AFR | 0.0057888 | 0.0052588 | 0.0061717 |
| 5 | AMR | 0.0069223 | 0.0068988 | 0.0075261 |
| 5 | EAS | 0.0099982 | 0.0101669 | 0.0106601 |
| 5 | EUR | 0.0066684 | 0.0066730 | 0.0069973 |
| 5 | SAS | 0.0092144 | 0.0090709 | 0.0098365 |
| 6 | AFR | 0.0052882 | 0.0048326 | 0.0056455 |
| 6 | AMR | 0.0063160 | 0.0062851 | 0.0067728 |
| 6 | EAS | 0.0089145 | 0.0090832 | 0.0094091 |
| 6 | EUR | 0.0059026 | 0.0058674 | 0.0061651 |
| 6 | SAS | 0.0082162 | 0.0081050 | 0.0087478 |
| 7 | AFR | 0.0061038 | 0.0056994 | 0.0065178 |
| 7 | AMR | 0.0072283 | 0.0071565 | 0.0077147 |
| 7 | EAS | 0.0103415 | 0.0104331 | 0.0108755 |
| 7 | EUR | 0.0067620 | 0.0068192 | 0.0070783 |
| 7 | SAS | 0.0093305 | 0.0092548 | 0.0099534 |
| 8 | AFR | 0.0057580 | 0.0052287 | 0.0062152 |
| 8 | AMR | 0.0072094 | 0.0072296 | 0.0078531 |
| 8 | EAS | 0.0103658 | 0.0105017 | 0.0108167 |
| 8 | EUR | 0.0066998 | 0.0067455 | 0.0070381 |
| 8 | SAS | 0.0090675 | 0.0089602 | 0.0097137 |
| 9 | AFR | 0.0072790 | 0.0067742 | 0.0076794 |
| 9 | AMR | 0.0082460 | 0.0081980 | 0.0088147 |
| 9 | EAS | 0.0119425 | 0.0122030 | 0.0124844 |
| 9 | EUR | 0.0081866 | 0.0081938 | 0.0084512 |
| 9 | SAS | 0.0107116 | 0.0105605 | 0.0113243 |
| 10 | AFR | 0.0060101 | 0.0055700 | 0.0063808 |
| 10 | AMR | 0.0070975 | 0.0070947 | 0.0075821 |
| 10 | EAS | 0.0099579 | 0.0102006 | 0.0105497 |
| 10 | EUR | 0.0067013 | 0.0067321 | 0.0069622 |
| 10 | SAS | 0.0092032 | 0.0092410 | 0.0098090 |
| 11 | AFR | 0.0057508 | 0.0052706 | 0.0061522 |
| 11 | AMR | 0.0071722 | 0.0071385 | 0.0076623 |
| 11 | EAS | 0.0100594 | 0.0102104 | 0.0106357 |
| 11 | EUR | 0.0066157 | 0.0066985 | 0.0069070 |
| 11 | SAS | 0.0093714 | 0.0093244 | 0.0099305 |
| 12 | AFR | 0.0058881 | 0.0053664 | 0.0062714 |
| 12 | AMR | 0.0071270 | 0.0071253 | 0.0076752 |
| 12 | EAS | 0.0102030 | 0.0104132 | 0.0108250 |
| 12 | EUR | 0.0067653 | 0.0067907 | 0.0071100 |
| 12 | SAS | 0.0096107 | 0.0093571 | 0.0103676 |
| 13 | AFR | 0.0057598 | 0.0052336 | 0.0061534 |
| 13 | AMR | 0.0067713 | 0.0067205 | 0.0073271 |
| 13 | EAS | 0.0099220 | 0.0101621 | 0.0104243 |
| 13 | EUR | 0.0066041 | 0.0066269 | 0.0069020 |
| 13 | SAS | 0.0088785 | 0.0090787 | 0.0096048 |
| 14 | AFR | 0.0063748 | 0.0059296 | 0.0068014 |
| 14 | AMR | 0.0078321 | 0.0078557 | 0.0084076 |
| 14 | EAS | 0.0105339 | 0.0109551 | 0.0112067 |
| 14 | EUR | 0.0071596 | 0.0072943 | 0.0075659 |
| 14 | SAS | 0.0098157 | 0.0097760 | 0.0104966 |
| 15 | AFR | 0.0073277 | 0.0069690 | 0.0077226 |
| 15 | AMR | 0.0083891 | 0.0084119 | 0.0089976 |
| 15 | EAS | 0.0120937 | 0.0123599 | 0.0127375 |
| 15 | EUR | 0.0084371 | 0.0084965 | 0.0087513 |
| 15 | SAS | 0.0109737 | 0.0111161 | 0.0118033 |
| 16 | AFR | 0.0073035 | 0.0069346 | 0.0077028 |
| 16 | AMR | 0.0087787 | 0.0087222 | 0.0094068 |
| 16 | EAS | 0.0125706 | 0.0127711 | 0.0131870 |
| 16 | EUR | 0.0081882 | 0.0084785 | 0.0087961 |
| 16 | SAS | 0.0113959 | 0.0109937 | 0.0119946 |
| 17 | AFR | 0.0073358 | 0.0070736 | 0.0078345 |
| 17 | AMR | 0.0087838 | 0.0088201 | 0.0093046 |
| 17 | EAS | 0.0129842 | 0.0131864 | 0.0135194 |
| 17 | EUR | 0.0084777 | 0.0086132 | 0.0088212 |
| 17 | SAS | 0.0115283 | 0.0116718 | 0.0121370 |
| 18 | AFR | 0.0059493 | 0.0055207 | 0.0064076 |
| 18 | AMR | 0.0074577 | 0.0074038 | 0.0080159 |
| 18 | EAS | 0.0107453 | 0.0110003 | 0.0112748 |
| 18 | EUR | 0.0070523 | 0.0071887 | 0.0073948 |
| 18 | SAS | 0.0095802 | 0.0095075 | 0.0101851 |
| 19 | AFR | 0.0070700 | 0.0067483 | 0.0073763 |
| 19 | AMR | 0.0083913 | 0.0084724 | 0.0088096 |
| 19 | EAS | 0.0121217 | 0.0122739 | 0.0126333 |
| 19 | EUR | 0.0080380 | 0.0081286 | 0.0082796 |
| 19 | SAS | 0.0106572 | 0.0105645 | 0.0112617 |
| 20 | AFR | 0.0070020 | 0.0066413 | 0.0073049 |
| 20 | AMR | 0.0087767 | 0.0088334 | 0.0092888 |
| 20 | EAS | 0.0127205 | 0.0130084 | 0.0132947 |
| 20 | EUR | 0.0080504 | 0.0082237 | 0.0083524 |
| 20 | SAS | 0.0110950 | 0.0110681 | 0.0116302 |
| 21 | AFR | 0.0081714 | 0.0078706 | 0.0086193 |
| 21 | AMR | 0.0089086 | 0.0090239 | 0.0095120 |
| 21 | EAS | 0.0118682 | 0.0120773 | 0.0123458 |
| 21 | EUR | 0.0085628 | 0.0087016 | 0.0089665 |
| 21 | SAS | 0.0110190 | 0.0110979 | 0.0116987 |
| 22 | AFR | 0.0090094 | 0.0088317 | 0.0093308 |
| 22 | AMR | 0.0100386 | 0.0102130 | 0.0105044 |
| 22 | EAS | 0.0139285 | 0.0143327 | 0.0143294 |
| 22 | EUR | 0.0096566 | 0.0098559 | 0.0100114 |
| 22 | SAS | 0.0126854 | 0.0128169 | 0.0133210 |
| 23 | AFR | 0.0018961 | 0.0023549 | 0.0019652 |
| 23 | AMR | 0.0023216 | 0.0027562 | 0.0024143 |
| 23 | EAS | 0.0047907 | 0.0056040 | 0.0047650 |
| 23 | EUR | 0.0027532 | 0.0032940 | 0.0028181 |
| 23 | SAS | 0.0036354 | 0.0043134 | 0.0036627 |
df_total_noth %>%
group_by(chrom) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
geom_point(size=3) +
theme_bw() +
xlab("Chromosome") +
ylab("Error Rate") +
labs(colour = "Method", shape = "Method") +
scale_colour_brewer(palette = "Set2") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
scale_x_continuous("Chromosome", labels = as.character(unique(df_total_noth$chrom)), breaks = unique(df_total_noth$chrom))

df_total_noth %>%
group_by(chrom, SUPER) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
geom_point(size=2) +
theme_bw() +
ylab("Error Rate") +
xlab("Chromosome") +
labs(colour = "Population", shape = "Method") +
scale_colour_brewer(palette = "Set1") +
scale_x_continuous("Chromosome", labels = as.character(unique(df_total_noth$chrom)), breaks = unique(df_total_noth$chrom))
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

In X, do we see large variation among samples?
df_total %>%
filter(chrom==23) %>%
select(Beagle, Eagle, SHAPEIT) %>% summary()
Beagle Eagle SHAPEIT
Min. :0.0004964 Min. :0.0008379 Min. :0.0005717
1st Qu.:0.0018688 1st Qu.:0.0023121 1st Qu.:0.0019586
Median :0.0029121 Median :0.0034861 Median :0.0029834
Mean :0.0030794 Mean :0.0036645 Mean :0.0031251
3rd Qu.:0.0041509 3rd Qu.:0.0048295 3rd Qu.:0.0041759
Max. :0.0065490 Max. :0.0074071 Max. :0.0065881
What range of values do we observe in the autosomes?
df_total_noth %>%
select(Beagle, Eagle, SHAPEIT) %>%
summarize(across(.cols = everything(),
.fns = list(
mean = ~mean(.x, na.rm =T),
sd = ~sd(.x, na.rm = T),
min = ~min(.x, na.rm=T),
max = ~max(.x, na.rm = T)
),
.names = "{.col}_{.fn}")
) %>%
knitr::kable()
| Beagle_mean | Beagle_sd | Beagle_min | Beagle_max | Eagle_mean | Eagle_sd | Eagle_min | Eagle_max | SHAPEIT_mean | SHAPEIT_sd | SHAPEIT_min | SHAPEIT_max |
|---|---|---|---|---|---|---|---|---|---|---|---|
| 0.0076089 | 0.0028562 | 0.0004964 | 0.0286303 | 0.0075472 | 0.0029323 | 0.0008379 | 0.0267024 | 0.0080498 | 0.002927 | 0.0005717 | 0.03858 |
df_total_noth %>%
select(chrom, Beagle, Eagle, SHAPEIT) %>%
group_by(chrom) %>%
summarize(across(.cols = everything(),
.fns = list(
mean = ~mean(.x, na.rm =T),
sd = ~sd(.x, na.rm = T),
min = ~min(.x, na.rm=T),
max = ~max(.x, na.rm = T)
),
.names = "{.col}_{.fn}")
) %>%
knitr::kable()
| chrom | Beagle_mean | Beagle_sd | Beagle_min | Beagle_max | Eagle_mean | Eagle_sd | Eagle_min | Eagle_max | SHAPEIT_mean | SHAPEIT_sd | SHAPEIT_min | SHAPEIT_max |
|---|---|---|---|---|---|---|---|---|---|---|---|---|
| 1 | 0.0076521 | 0.0023322 | 0.0023801 | 0.0136999 | 0.0074991 | 0.0025325 | 0.0030514 | 0.0139830 | 0.0081145 | 0.0023436 | 0.0027549 | 0.0144356 |
| 2 | 0.0076647 | 0.0023303 | 0.0029286 | 0.0133430 | 0.0074667 | 0.0025172 | 0.0023141 | 0.0139171 | 0.0081643 | 0.0023535 | 0.0040192 | 0.0141955 |
| 3 | 0.0071878 | 0.0022068 | 0.0018160 | 0.0127320 | 0.0070196 | 0.0023905 | 0.0022519 | 0.0128360 | 0.0076684 | 0.0022175 | 0.0026375 | 0.0137675 |
| 4 | 0.0067061 | 0.0020228 | 0.0023847 | 0.0117561 | 0.0065728 | 0.0022239 | 0.0020223 | 0.0122799 | 0.0071506 | 0.0020349 | 0.0026897 | 0.0118537 |
| 5 | 0.0071902 | 0.0022701 | 0.0027259 | 0.0126031 | 0.0070086 | 0.0024388 | 0.0019837 | 0.0127815 | 0.0076810 | 0.0023090 | 0.0033045 | 0.0130985 |
| 6 | 0.0064784 | 0.0019903 | 0.0019080 | 0.0132438 | 0.0063175 | 0.0021561 | 0.0017240 | 0.0132704 | 0.0068826 | 0.0019991 | 0.0023244 | 0.0135365 |
| 7 | 0.0074391 | 0.0022364 | 0.0029074 | 0.0150164 | 0.0072982 | 0.0023531 | 0.0028348 | 0.0135418 | 0.0078961 | 0.0022286 | 0.0030710 | 0.0146751 |
| 8 | 0.0072741 | 0.0023261 | 0.0028526 | 0.0135109 | 0.0071112 | 0.0025080 | 0.0026864 | 0.0137193 | 0.0077785 | 0.0023149 | 0.0035202 | 0.0149419 |
| 9 | 0.0087028 | 0.0024156 | 0.0037646 | 0.0145061 | 0.0085344 | 0.0026200 | 0.0038298 | 0.0152881 | 0.0091643 | 0.0024335 | 0.0041561 | 0.0151824 |
| 10 | 0.0073034 | 0.0021106 | 0.0023978 | 0.0123300 | 0.0071957 | 0.0022981 | 0.0022696 | 0.0126610 | 0.0077402 | 0.0021356 | 0.0033953 | 0.0129421 |
| 11 | 0.0072545 | 0.0023517 | 0.0024552 | 0.0132898 | 0.0071127 | 0.0025089 | 0.0021710 | 0.0137564 | 0.0076998 | 0.0023498 | 0.0029189 | 0.0138887 |
| 12 | 0.0073676 | 0.0024640 | 0.0031297 | 0.0286303 | 0.0071869 | 0.0025879 | 0.0026982 | 0.0267024 | 0.0078629 | 0.0026569 | 0.0032827 | 0.0385800 |
| 13 | 0.0070782 | 0.0022524 | 0.0022073 | 0.0127083 | 0.0069520 | 0.0024339 | 0.0020488 | 0.0133164 | 0.0075517 | 0.0022353 | 0.0034269 | 0.0134057 |
| 14 | 0.0078292 | 0.0023410 | 0.0023962 | 0.0159714 | 0.0077546 | 0.0025490 | 0.0022465 | 0.0166544 | 0.0083515 | 0.0024001 | 0.0031900 | 0.0157087 |
| 15 | 0.0088513 | 0.0026191 | 0.0025277 | 0.0165449 | 0.0087992 | 0.0027724 | 0.0028078 | 0.0174337 | 0.0093716 | 0.0026636 | 0.0032533 | 0.0174043 |
| 16 | 0.0090042 | 0.0028986 | 0.0025181 | 0.0173381 | 0.0088870 | 0.0029658 | 0.0026695 | 0.0169698 | 0.0095468 | 0.0029068 | 0.0035420 | 0.0177347 |
| 17 | 0.0091358 | 0.0029524 | 0.0030712 | 0.0173353 | 0.0091251 | 0.0030734 | 0.0028818 | 0.0176482 | 0.0096319 | 0.0029560 | 0.0035134 | 0.0174917 |
| 18 | 0.0075749 | 0.0024421 | 0.0019858 | 0.0141914 | 0.0074640 | 0.0025959 | 0.0021564 | 0.0147436 | 0.0080646 | 0.0024261 | 0.0028701 | 0.0144952 |
| 19 | 0.0086534 | 0.0026488 | 0.0010857 | 0.0154416 | 0.0085857 | 0.0027182 | 0.0021404 | 0.0154304 | 0.0090404 | 0.0027148 | 0.0011167 | 0.0169087 |
| 20 | 0.0088541 | 0.0029581 | 0.0029367 | 0.0205275 | 0.0088080 | 0.0031023 | 0.0029535 | 0.0219209 | 0.0092697 | 0.0029872 | 0.0033721 | 0.0209013 |
| 21 | 0.0092530 | 0.0024265 | 0.0032546 | 0.0181752 | 0.0092396 | 0.0025532 | 0.0037141 | 0.0161322 | 0.0097647 | 0.0024139 | 0.0041352 | 0.0164855 |
| 22 | 0.0104660 | 0.0029920 | 0.0026342 | 0.0211825 | 0.0105487 | 0.0031360 | 0.0037631 | 0.0219650 | 0.0108801 | 0.0030757 | 0.0034809 | 0.0223834 |
| 23 | 0.0030794 | 0.0013598 | 0.0004964 | 0.0065490 | 0.0036645 | 0.0014956 | 0.0008379 | 0.0074071 | 0.0031251 | 0.0013461 | 0.0005717 | 0.0065881 |
Let’s first do a hypothesis test to compare the mean error rates in X versus the autosomes.
# Beagle
autosomes <- df_total_noth %>% filter(chrom < 23) %>% pull(Beagle)
chrX <- df_total_noth %>% filter(chrom == 23) %>% pull(Beagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 0.00487 0.00795 0.00308 100. 0 1638. 0.00478 0.00497
# ℹ 2 more variables: method <chr>, alternative <chr>
# Eagle
autosomes <- df_total_noth %>% filter(chrom < 23) %>% pull(Eagle)
chrX <- df_total_noth %>% filter(chrom == 23) %>% pull(Eagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 0.00418 0.00784 0.00366 78.5 0 1591. 0.00407 0.00428
# ℹ 2 more variables: method <chr>, alternative <chr>
# SHAPEIT
autosomes <- df_total_noth %>% filter(chrom < 23) %>% pull(SHAPEIT)
chrX <- df_total_noth %>% filter(chrom == 23) %>% pull(SHAPEIT)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 0.00530 0.00842 0.00313 109. 0 1667. 0.00520 0.00539
# ℹ 2 more variables: method <chr>, alternative <chr>
Additionally, I would like to test the null hypothesis that the error rates are the same across chromosomes for each method:
mod_fit <- df_total_noth %>%
filter(chrom < 23) %>%
{lmerTest::lmer(Beagle ~ chrom + (1|pair_id), data = .)}
df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(method = "Beagle")
Warning in tidy.anova(.): The following column names in ANOVA output were not
recognized or transformed: NumDF, DenDF
mod_fit <- df_total_noth %>%
filter(chrom < 23) %>%
{lmerTest::lmer(Eagle ~ chrom + (1|pair_id), data = .)}
df_anova <- bind_rows(df_anova, {anova(mod_fit) %>% broom::tidy() %>% mutate(method = "Eagle")})
Warning in tidy.anova(.): The following column names in ANOVA output were not
recognized or transformed: NumDF, DenDF
mod_fit <- df_total_noth %>%
filter(chrom < 23) %>%
{lmerTest::lmer(SHAPEIT ~ chrom + (1|pair_id), data = .)}
df_anova <- bind_rows(df_anova, {anova(mod_fit) %>% broom::tidy() %>% mutate(method = "SHAPEIT")})
Warning in tidy.anova(.): The following column names in ANOVA output were not
recognized or transformed: NumDF, DenDF
df_anova %>%
knitr::kable()
| term | sumsq | meansq | NumDF | DenDF | statistic | p.value | method |
|---|---|---|---|---|---|---|---|
| chrom | 0.0068825 | 0.0068825 | 1 | 12641 | 4603.281 | 0 | Beagle |
| chrom | 0.0079801 | 0.0079801 | 1 | 12641 | 5635.171 | 0 | Eagle |
| chrom | 0.0068546 | 0.0068546 | 1 | 12641 | 4397.972 | 0 | SHAPEIT |
For each chromosome, we will test several hypotheses:
For the first test, I’ll use a linear mixed model with random intercepts for each individual/synthetic diploid. This will also allow me to do contrasts for the pairwise comparisons.
mod_fit <- df_total_noth %>%
filter(chrom == 1) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)
df_pairwise <- emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
for(i in 2:23){
mod_fit <- df_total_noth %>%
filter(chrom == i) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
df_anova <- df_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
df_pairwise <- df_pairwise %>% bind_rows({
emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
}
df_anova %>% knitr::kable()
| term | sumsq | meansq | NumDF | DenDF | statistic | p.value | chrom |
|---|---|---|---|---|---|---|---|
| method | 0.0001236 | 0.0000618 | 2 | 1202 | 656.00360 | 0 | 1 |
| method | 0.0001556 | 0.0000778 | 2 | 1202 | 823.78246 | 0 | 2 |
| method | 0.0001365 | 0.0000682 | 2 | 1202 | 733.34212 | 0 | 3 |
| method | 0.0001102 | 0.0000551 | 2 | 1202 | 559.83128 | 0 | 4 |
| method | 0.0001456 | 0.0000728 | 2 | 1202 | 731.43837 | 0 | 5 |
| method | 0.0001020 | 0.0000510 | 2 | 1202 | 629.02561 | 0 | 6 |
| method | 0.0001176 | 0.0000588 | 2 | 1202 | 576.07381 | 0 | 7 |
| method | 0.0001457 | 0.0000729 | 2 | 1202 | 494.42277 | 0 | 8 |
| method | 0.0001280 | 0.0000640 | 2 | 1202 | 496.03954 | 0 | 9 |
| method | 0.0001001 | 0.0000500 | 2 | 1202 | 462.22172 | 0 | 10 |
| method | 0.0001130 | 0.0000565 | 2 | 1202 | 463.45512 | 0 | 11 |
| method | 0.0001475 | 0.0000737 | 2 | 1202 | 406.63922 | 0 | 12 |
| method | 0.0001203 | 0.0000602 | 2 | 1202 | 340.63110 | 0 | 13 |
| method | 0.0001273 | 0.0000637 | 2 | 1202 | 405.14772 | 0 | 14 |
| method | 0.0001206 | 0.0000603 | 2 | 1202 | 368.10822 | 0 | 15 |
| method | 0.0001492 | 0.0000746 | 2 | 1202 | 299.00932 | 0 | 16 |
| method | 0.0001009 | 0.0000505 | 2 | 1202 | 245.86294 | 0 | 17 |
| method | 0.0001230 | 0.0000615 | 2 | 1202 | 414.98049 | 0 | 18 |
| method | 0.0000725 | 0.0000362 | 2 | 1202 | 181.45836 | 0 | 19 |
| method | 0.0000779 | 0.0000389 | 2 | 1202 | 207.08658 | 0 | 20 |
| method | 0.0001079 | 0.0000540 | 2 | 1202 | 220.66307 | 0 | 21 |
| method | 0.0000578 | 0.0000289 | 2 | 1202 | 96.57538 | 0 | 22 |
| method | 0.0002118 | 0.0001059 | 2 | 1998 | 2542.00116 | 0 | 23 |
df_pairwise %>% knitr::kable()
| term | contrast | null.value | estimate | std.error | df | statistic | adj.p.value | chrom |
|---|---|---|---|---|---|---|---|---|
| method | Beagle - Eagle | 0 | 0.0001530 | 1.77e-05 | 1202 | 8.6488600 | 0.0000000 | 1 |
| method | Beagle - SHAPEIT | 0 | -0.0004624 | 1.77e-05 | 1202 | -26.1370756 | 0.0000000 | 1 |
| method | Eagle - SHAPEIT | 0 | -0.0006154 | 1.77e-05 | 1202 | -34.7859356 | 0.0000000 | 1 |
| method | Beagle - Eagle | 0 | 0.0001980 | 1.77e-05 | 1202 | 11.1769601 | 0.0000000 | 2 |
| method | Beagle - SHAPEIT | 0 | -0.0004996 | 1.77e-05 | 1202 | -28.2047198 | 0.0000000 | 2 |
| method | Eagle - SHAPEIT | 0 | -0.0006976 | 1.77e-05 | 1202 | -39.3816799 | 0.0000000 | 2 |
| method | Beagle - Eagle | 0 | 0.0001682 | 1.76e-05 | 1202 | 9.5679959 | 0.0000000 | 3 |
| method | Beagle - SHAPEIT | 0 | -0.0004806 | 1.76e-05 | 1202 | -27.3306914 | 0.0000000 | 3 |
| method | Eagle - SHAPEIT | 0 | -0.0006488 | 1.76e-05 | 1202 | -36.8986873 | 0.0000000 | 3 |
| method | Beagle - Eagle | 0 | 0.0001333 | 1.81e-05 | 1202 | 7.3721385 | 0.0000000 | 4 |
| method | Beagle - SHAPEIT | 0 | -0.0004445 | 1.81e-05 | 1202 | -24.5802640 | 0.0000000 | 4 |
| method | Eagle - SHAPEIT | 0 | -0.0005778 | 1.81e-05 | 1202 | -31.9524025 | 0.0000000 | 4 |
| method | Beagle - Eagle | 0 | 0.0001816 | 1.82e-05 | 1202 | 9.9851073 | 0.0000000 | 5 |
| method | Beagle - SHAPEIT | 0 | -0.0004907 | 1.82e-05 | 1202 | -26.9821360 | 0.0000000 | 5 |
| method | Eagle - SHAPEIT | 0 | -0.0006723 | 1.82e-05 | 1202 | -36.9672433 | 0.0000000 | 5 |
| method | Beagle - Eagle | 0 | 0.0001609 | 1.64e-05 | 1202 | 9.8033434 | 0.0000000 | 6 |
| method | Beagle - SHAPEIT | 0 | -0.0004041 | 1.64e-05 | 1202 | -24.6188170 | 0.0000000 | 6 |
| method | Eagle - SHAPEIT | 0 | -0.0005651 | 1.64e-05 | 1202 | -34.4221605 | 0.0000000 | 6 |
| method | Beagle - Eagle | 0 | 0.0001409 | 1.84e-05 | 1202 | 7.6532132 | 0.0000000 | 7 |
| method | Beagle - SHAPEIT | 0 | -0.0004569 | 1.84e-05 | 1202 | -24.8122126 | 0.0000000 | 7 |
| method | Eagle - SHAPEIT | 0 | -0.0005979 | 1.84e-05 | 1202 | -32.4654258 | 0.0000000 | 7 |
| method | Beagle - Eagle | 0 | 0.0001629 | 2.21e-05 | 1202 | 7.3614752 | 0.0000000 | 8 |
| method | Beagle - SHAPEIT | 0 | -0.0005044 | 2.21e-05 | 1202 | -22.7954906 | 0.0000000 | 8 |
| method | Eagle - SHAPEIT | 0 | -0.0006673 | 2.21e-05 | 1202 | -30.1569658 | 0.0000000 | 8 |
| method | Beagle - Eagle | 0 | 0.0001684 | 2.07e-05 | 1202 | 8.1314831 | 0.0000000 | 9 |
| method | Beagle - SHAPEIT | 0 | -0.0004615 | 2.07e-05 | 1202 | -22.2870296 | 0.0000000 | 9 |
| method | Eagle - SHAPEIT | 0 | -0.0006299 | 2.07e-05 | 1202 | -30.4185127 | 0.0000000 | 9 |
| method | Beagle - Eagle | 0 | 0.0001077 | 1.90e-05 | 1202 | 5.6775925 | 0.0000001 | 10 |
| method | Beagle - SHAPEIT | 0 | -0.0004368 | 1.90e-05 | 1202 | -23.0292590 | 0.0000000 | 10 |
| method | Eagle - SHAPEIT | 0 | -0.0005445 | 1.90e-05 | 1202 | -28.7068515 | 0.0000000 | 10 |
| method | Beagle - Eagle | 0 | 0.0001419 | 2.01e-05 | 1202 | 7.0497074 | 0.0000000 | 11 |
| method | Beagle - SHAPEIT | 0 | -0.0004452 | 2.01e-05 | 1202 | -22.1248811 | 0.0000000 | 11 |
| method | Eagle - SHAPEIT | 0 | -0.0005871 | 2.01e-05 | 1202 | -29.1745885 | 0.0000000 | 11 |
| method | Beagle - Eagle | 0 | 0.0001807 | 2.45e-05 | 1202 | 7.3622141 | 0.0000000 | 12 |
| method | Beagle - SHAPEIT | 0 | -0.0004953 | 2.45e-05 | 1202 | -20.1790520 | 0.0000000 | 12 |
| method | Eagle - SHAPEIT | 0 | -0.0006760 | 2.45e-05 | 1202 | -27.5412661 | 0.0000000 | 12 |
| method | Beagle - Eagle | 0 | 0.0001262 | 2.42e-05 | 1202 | 5.2086356 | 0.0000007 | 13 |
| method | Beagle - SHAPEIT | 0 | -0.0004735 | 2.42e-05 | 1202 | -19.5451570 | 0.0000000 | 13 |
| method | Eagle - SHAPEIT | 0 | -0.0005997 | 2.42e-05 | 1202 | -24.7537925 | 0.0000000 | 13 |
| method | Beagle - Eagle | 0 | 0.0000746 | 2.28e-05 | 1202 | 3.2639710 | 0.0032378 | 14 |
| method | Beagle - SHAPEIT | 0 | -0.0005222 | 2.28e-05 | 1202 | -22.8574295 | 0.0000000 | 14 |
| method | Eagle - SHAPEIT | 0 | -0.0005968 | 2.28e-05 | 1202 | -26.1214005 | 0.0000000 | 14 |
| method | Beagle - Eagle | 0 | 0.0000521 | 2.33e-05 | 1202 | 2.2312906 | 0.0664182 | 15 |
| method | Beagle - SHAPEIT | 0 | -0.0005203 | 2.33e-05 | 1202 | -22.3029015 | 0.0000000 | 15 |
| method | Eagle - SHAPEIT | 0 | -0.0005724 | 2.33e-05 | 1202 | -24.5341921 | 0.0000000 | 15 |
| method | Beagle - Eagle | 0 | 0.0001172 | 2.88e-05 | 1202 | 4.0717243 | 0.0001470 | 16 |
| method | Beagle - SHAPEIT | 0 | -0.0005426 | 2.88e-05 | 1202 | -18.8466611 | 0.0000000 | 16 |
| method | Eagle - SHAPEIT | 0 | -0.0006598 | 2.88e-05 | 1202 | -22.9183854 | 0.0000000 | 16 |
| method | Beagle - Eagle | 0 | 0.0000108 | 2.61e-05 | 1202 | 0.4119101 | 0.9107351 | 17 |
| method | Beagle - SHAPEIT | 0 | -0.0004960 | 2.61e-05 | 1202 | -18.9947521 | 0.0000000 | 17 |
| method | Eagle - SHAPEIT | 0 | -0.0005068 | 2.61e-05 | 1202 | -19.4066622 | 0.0000000 | 17 |
| method | Beagle - Eagle | 0 | 0.0001109 | 2.22e-05 | 1202 | 4.9985018 | 0.0000020 | 18 |
| method | Beagle - SHAPEIT | 0 | -0.0004897 | 2.22e-05 | 1202 | -22.0717069 | 0.0000000 | 18 |
| method | Eagle - SHAPEIT | 0 | -0.0006006 | 2.22e-05 | 1202 | -27.0702087 | 0.0000000 | 18 |
| method | Beagle - Eagle | 0 | 0.0000677 | 2.58e-05 | 1202 | 2.6289886 | 0.0235566 | 19 |
| method | Beagle - SHAPEIT | 0 | -0.0003870 | 2.58e-05 | 1202 | -15.0257580 | 0.0000000 | 19 |
| method | Eagle - SHAPEIT | 0 | -0.0004547 | 2.58e-05 | 1202 | -17.6547467 | 0.0000000 | 19 |
| method | Beagle - Eagle | 0 | 0.0000461 | 2.50e-05 | 1202 | 1.8443352 | 0.1557312 | 20 |
| method | Beagle - SHAPEIT | 0 | -0.0004156 | 2.50e-05 | 1202 | -16.6300028 | 0.0000000 | 20 |
| method | Eagle - SHAPEIT | 0 | -0.0004617 | 2.50e-05 | 1202 | -18.4743380 | 0.0000000 | 20 |
| method | Beagle - Eagle | 0 | 0.0000134 | 2.85e-05 | 1202 | 0.4700150 | 0.8853898 | 21 |
| method | Beagle - SHAPEIT | 0 | -0.0005117 | 2.85e-05 | 1202 | -17.9536956 | 0.0000000 | 21 |
| method | Eagle - SHAPEIT | 0 | -0.0005251 | 2.85e-05 | 1202 | -18.4237107 | 0.0000000 | 21 |
| method | Beagle - Eagle | 0 | -0.0000827 | 3.15e-05 | 1202 | -2.6225872 | 0.0239835 | 22 |
| method | Beagle - SHAPEIT | 0 | -0.0004141 | 3.15e-05 | 1202 | -13.1309636 | 0.0000000 | 22 |
| method | Eagle - SHAPEIT | 0 | -0.0003314 | 3.15e-05 | 1202 | -10.5083765 | 0.0000000 | 22 |
| method | Beagle - Eagle | 0 | -0.0005851 | 9.10e-06 | 1998 | -64.0995718 | 0.0000000 | 23 |
| method | Beagle - SHAPEIT | 0 | -0.0000457 | 9.10e-06 | 1998 | -5.0047233 | 0.0000018 | 23 |
| method | Eagle - SHAPEIT | 0 | 0.0005394 | 9.10e-06 | 1998 | 59.0948484 | 0.0000000 | 23 |
df_pairwise %>%
filter(adj.p.value > 0.05) %>%
knitr::kable()
| term | contrast | null.value | estimate | std.error | df | statistic | adj.p.value | chrom |
|---|---|---|---|---|---|---|---|---|
| method | Beagle - Eagle | 0 | 5.21e-05 | 2.33e-05 | 1202 | 2.2312906 | 0.0664182 | 15 |
| method | Beagle - Eagle | 0 | 1.08e-05 | 2.61e-05 | 1202 | 0.4119101 | 0.9107351 | 17 |
| method | Beagle - Eagle | 0 | 4.61e-05 | 2.50e-05 | 1202 | 1.8443352 | 0.1557312 | 20 |
| method | Beagle - Eagle | 0 | 1.34e-05 | 2.85e-05 | 1202 | 0.4700150 | 0.8853898 | 21 |
Now let’s do these comparisons within each super-population:
mod_fit <- df_total_noth %>%
filter(chrom == 1) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
df_pop_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)
df_pop_pairwise <- emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
df_pop_pop <- emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = 1)
for(i in 2:23){
mod_fit <- df_total_noth %>%
filter(chrom == i) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
df_pop_anova <- df_pop_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
df_pop_pairwise <- df_pop_pairwise %>% bind_rows({
emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
df_pop_pop <- df_pop_pop %>% bind_rows({
emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = i)})
}
df_pop_anova %>% knitr::kable()
| term | sumsq | meansq | NumDF | DenDF | statistic | p.value | chrom |
|---|---|---|---|---|---|---|---|
| method | 0.0000970 | 0.0000485 | 2 | 1194.0000 | 684.993557 | 0 | 1 |
| SUPER | 0.0000403 | 0.0000101 | 4 | 597.0000 | 142.135219 | 0 | 1 |
| method:SUPER | 0.0000287 | 0.0000036 | 8 | 1194.0000 | 50.640353 | 0 | 1 |
| method | 0.0001270 | 0.0000635 | 2 | 1194.0000 | 834.414662 | 0 | 2 |
| SUPER | 0.0000456 | 0.0000114 | 4 | 597.0000 | 149.664197 | 0 | 2 |
| method:SUPER | 0.0000226 | 0.0000028 | 8 | 1194.0000 | 37.178475 | 0 | 2 |
| method | 0.0001072 | 0.0000536 | 2 | 1194.0000 | 751.821151 | 0 | 3 |
| SUPER | 0.0000396 | 0.0000099 | 4 | 597.0000 | 138.951458 | 0 | 3 |
| method:SUPER | 0.0000267 | 0.0000033 | 8 | 1194.0000 | 46.847777 | 0 | 3 |
| method | 0.0000892 | 0.0000446 | 2 | 1194.0000 | 577.945676 | 0 | 4 |
| SUPER | 0.0000448 | 0.0000112 | 4 | 597.0000 | 145.126286 | 0 | 4 |
| method:SUPER | 0.0000261 | 0.0000033 | 8 | 1194.0000 | 42.270907 | 0 | 4 |
| method | 0.0001184 | 0.0000592 | 2 | 1194.0000 | 756.839178 | 0 | 5 |
| SUPER | 0.0000413 | 0.0000103 | 4 | 597.0000 | 131.905501 | 0 | 5 |
| method:SUPER | 0.0000263 | 0.0000033 | 8 | 1194.0000 | 42.028809 | 0 | 5 |
| method | 0.0000792 | 0.0000396 | 2 | 1194.0000 | 609.514893 | 0 | 6 |
| SUPER | 0.0000322 | 0.0000081 | 4 | 597.0000 | 124.060370 | 0 | 6 |
| method:SUPER | 0.0000200 | 0.0000025 | 8 | 1194.0000 | 38.422997 | 0 | 6 |
| method | 0.0000952 | 0.0000476 | 2 | 1194.0000 | 541.823084 | 0 | 7 |
| SUPER | 0.0000468 | 0.0000117 | 4 | 596.9999 | 133.235429 | 0 | 7 |
| method:SUPER | 0.0000178 | 0.0000022 | 8 | 1194.0000 | 25.282506 | 0 | 7 |
| method | 0.0001089 | 0.0000545 | 2 | 1194.0000 | 448.195973 | 0 | 8 |
| SUPER | 0.0000662 | 0.0000166 | 4 | 597.0000 | 136.218054 | 0 | 8 |
| method:SUPER | 0.0000321 | 0.0000040 | 8 | 1194.0000 | 32.986322 | 0 | 8 |
| method | 0.0000978 | 0.0000489 | 2 | 1194.0000 | 467.435725 | 0 | 9 |
| SUPER | 0.0000558 | 0.0000139 | 4 | 597.0000 | 133.284760 | 0 | 9 |
| method:SUPER | 0.0000302 | 0.0000038 | 8 | 1194.0000 | 36.062684 | 0 | 9 |
| method | 0.0000800 | 0.0000400 | 2 | 1194.0000 | 451.764809 | 0 | 10 |
| SUPER | 0.0000498 | 0.0000124 | 4 | 596.9999 | 140.515094 | 0 | 10 |
| method:SUPER | 0.0000244 | 0.0000030 | 8 | 1194.0000 | 34.400393 | 0 | 10 |
| method | 0.0000880 | 0.0000440 | 2 | 1194.0000 | 435.589782 | 0 | 11 |
| SUPER | 0.0000532 | 0.0000133 | 4 | 596.9999 | 131.798942 | 0 | 11 |
| method:SUPER | 0.0000259 | 0.0000032 | 8 | 1194.0000 | 32.068560 | 0 | 11 |
| method | 0.0001238 | 0.0000619 | 2 | 1194.0001 | 398.164349 | 0 | 12 |
| SUPER | 0.0000701 | 0.0000175 | 4 | 596.9996 | 112.723771 | 0 | 12 |
| method:SUPER | 0.0000323 | 0.0000040 | 8 | 1194.0001 | 25.975115 | 0 | 12 |
| method | 0.0000906 | 0.0000453 | 2 | 1194.0000 | 305.359265 | 0 | 13 |
| SUPER | 0.0000761 | 0.0000190 | 4 | 597.0000 | 128.286830 | 0 | 13 |
| method:SUPER | 0.0000352 | 0.0000044 | 8 | 1194.0000 | 29.645340 | 0 | 13 |
| method | 0.0001040 | 0.0000520 | 2 | 1194.0000 | 395.555364 | 0 | 14 |
| SUPER | 0.0000617 | 0.0000154 | 4 | 597.0000 | 117.352113 | 0 | 14 |
| method:SUPER | 0.0000318 | 0.0000040 | 8 | 1194.0000 | 30.269096 | 0 | 14 |
| method | 0.0001049 | 0.0000524 | 2 | 1194.0000 | 361.313934 | 0 | 15 |
| SUPER | 0.0000679 | 0.0000170 | 4 | 597.0000 | 116.984755 | 0 | 15 |
| method:SUPER | 0.0000236 | 0.0000029 | 8 | 1194.0000 | 20.318197 | 0 | 15 |
| method | 0.0001297 | 0.0000649 | 2 | 1194.0000 | 283.660734 | 0 | 16 |
| SUPER | 0.0001029 | 0.0000257 | 4 | 596.9999 | 112.494890 | 0 | 16 |
| method:SUPER | 0.0000269 | 0.0000034 | 8 | 1194.0000 | 14.684099 | 0 | 16 |
| method | 0.0000805 | 0.0000403 | 2 | 1194.0000 | 208.716218 | 0 | 17 |
| SUPER | 0.0000959 | 0.0000240 | 4 | 597.0000 | 124.243178 | 0 | 17 |
| method:SUPER | 0.0000164 | 0.0000021 | 8 | 1194.0000 | 10.644324 | 0 | 17 |
| method | 0.0000938 | 0.0000469 | 2 | 1194.0000 | 372.147639 | 0 | 18 |
| SUPER | 0.0000713 | 0.0000178 | 4 | 597.0000 | 141.355742 | 0 | 18 |
| method:SUPER | 0.0000276 | 0.0000034 | 8 | 1194.0000 | 27.352646 | 0 | 18 |
| method | 0.0000639 | 0.0000320 | 2 | 1194.0000 | 172.053799 | 0 | 19 |
| SUPER | 0.0000894 | 0.0000223 | 4 | 597.0000 | 120.274053 | 0 | 19 |
| method:SUPER | 0.0000182 | 0.0000023 | 8 | 1194.0000 | 12.225247 | 0 | 19 |
| method | 0.0000661 | 0.0000330 | 2 | 1194.0000 | 193.320266 | 0 | 20 |
| SUPER | 0.0000866 | 0.0000217 | 4 | 597.0000 | 126.782913 | 0 | 20 |
| method:SUPER | 0.0000220 | 0.0000027 | 8 | 1194.0000 | 16.080003 | 0 | 20 |
| method | 0.0000882 | 0.0000441 | 2 | 1194.0000 | 190.791026 | 0 | 21 |
| SUPER | 0.0000665 | 0.0000166 | 4 | 597.0000 | 71.906930 | 0 | 21 |
| method:SUPER | 0.0000180 | 0.0000023 | 8 | 1194.0000 | 9.744354 | 0 | 21 |
| method | 0.0000520 | 0.0000260 | 2 | 1194.0000 | 90.499127 | 0 | 22 |
| SUPER | 0.0000934 | 0.0000234 | 4 | 597.0000 | 81.308769 | 0 | 22 |
| method:SUPER | 0.0000168 | 0.0000021 | 8 | 1194.0000 | 7.295923 | 0 | 22 |
| method | 0.0002118 | 0.0001059 | 2 | 1990.0000 | 3255.331545 | 0 | 23 |
| SUPER | 0.0000458 | 0.0000114 | 4 | 994.9999 | 351.584878 | 0 | 23 |
| method:SUPER | 0.0000185 | 0.0000023 | 8 | 1990.0000 | 71.084254 | 0 | 23 |
df_pop_pairwise %>% knitr::kable()
| SUPER | term | contrast | null.value | estimate | std.error | df | statistic | adj.p.value | chrom |
|---|---|---|---|---|---|---|---|---|---|
| AFR | method | Beagle - Eagle | 0 | 0.0005055 | 2.65e-05 | 1194 | 19.0440527 | 0.0000000 | 1 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003773 | 2.65e-05 | 1194 | -14.2151091 | 0.0000000 | 1 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0008828 | 2.65e-05 | 1194 | -33.2591618 | 0.0000000 | 1 |
| AMR | method | Beagle - Eagle | 0 | 0.0000373 | 3.22e-05 | 1194 | 1.1614326 | 0.4765626 | 1 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005463 | 3.22e-05 | 1194 | -16.9923411 | 0.0000000 | 1 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0005837 | 3.22e-05 | 1194 | -18.1537736 | 0.0000000 | 1 |
| EAS | method | Beagle - Eagle | 0 | -0.0002248 | 4.44e-05 | 1194 | -5.0678399 | 0.0000014 | 1 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005496 | 4.44e-05 | 1194 | -12.3933265 | 0.0000000 | 1 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0003249 | 4.44e-05 | 1194 | -7.3254866 | 0.0000000 | 1 |
| EUR | method | Beagle - Eagle | 0 | -0.0000480 | 3.64e-05 | 1194 | -1.3200650 | 0.3842343 | 1 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003049 | 3.64e-05 | 1194 | -8.3808704 | 0.0000000 | 1 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002569 | 3.64e-05 | 1194 | -7.0608053 | 0.0000000 | 1 |
| SAS | method | Beagle - Eagle | 0 | 0.0000789 | 4.08e-05 | 1194 | 1.9338974 | 0.1296453 | 1 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006526 | 4.08e-05 | 1194 | -15.9880567 | 0.0000000 | 1 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0007315 | 4.08e-05 | 1194 | -17.9219541 | 0.0000000 | 1 |
| AFR | method | Beagle - Eagle | 0 | 0.0005163 | 2.75e-05 | 1194 | 18.7620053 | 0.0000000 | 2 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004220 | 2.75e-05 | 1194 | -15.3352301 | 0.0000000 | 2 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0009383 | 2.75e-05 | 1194 | -34.0972354 | 0.0000000 | 2 |
| AMR | method | Beagle - Eagle | 0 | 0.0000877 | 3.33e-05 | 1194 | 2.6305211 | 0.0234572 | 2 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005233 | 3.33e-05 | 1194 | -15.7005189 | 0.0000000 | 2 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0006110 | 3.33e-05 | 1194 | -18.3310400 | 0.0000000 | 2 |
| EAS | method | Beagle - Eagle | 0 | -0.0001726 | 4.60e-05 | 1194 | -3.7529039 | 0.0005369 | 2 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006795 | 4.60e-05 | 1194 | -14.7788721 | 0.0000000 | 2 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0005070 | 4.60e-05 | 1194 | -11.0259682 | 0.0000000 | 2 |
| EUR | method | Beagle - Eagle | 0 | 0.0000276 | 3.77e-05 | 1194 | 0.7308715 | 0.7452005 | 2 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003749 | 3.77e-05 | 1194 | -9.9396659 | 0.0000000 | 2 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0004025 | 3.77e-05 | 1194 | -10.6705374 | 0.0000000 | 2 |
| SAS | method | Beagle - Eagle | 0 | 0.0001513 | 4.23e-05 | 1194 | 3.5759958 | 0.0010564 | 2 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006492 | 4.23e-05 | 1194 | -15.3418032 | 0.0000000 | 2 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0008006 | 4.23e-05 | 1194 | -18.9177990 | 0.0000000 | 2 |
| AFR | method | Beagle - Eagle | 0 | 0.0005019 | 2.66e-05 | 1194 | 18.8439898 | 0.0000000 | 3 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004184 | 2.66e-05 | 1194 | -15.7075197 | 0.0000000 | 3 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0009203 | 2.66e-05 | 1194 | -34.5515095 | 0.0000000 | 3 |
| AMR | method | Beagle - Eagle | 0 | 0.0000697 | 3.23e-05 | 1194 | 2.1604475 | 0.0785432 | 3 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005212 | 3.23e-05 | 1194 | -16.1544877 | 0.0000000 | 3 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0005909 | 3.23e-05 | 1194 | -18.3149352 | 0.0000000 | 3 |
| EAS | method | Beagle - Eagle | 0 | -0.0002182 | 4.45e-05 | 1194 | -4.9020919 | 0.0000032 | 3 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005701 | 4.45e-05 | 1194 | -12.8090854 | 0.0000000 | 3 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0003519 | 4.45e-05 | 1194 | -7.9069935 | 0.0000000 | 3 |
| EUR | method | Beagle - Eagle | 0 | -0.0000314 | 3.65e-05 | 1194 | -0.8600196 | 0.6656372 | 3 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003447 | 3.65e-05 | 1194 | -9.4407418 | 0.0000000 | 3 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0003133 | 3.65e-05 | 1194 | -8.5807222 | 0.0000000 | 3 |
| SAS | method | Beagle - Eagle | 0 | 0.0001166 | 4.10e-05 | 1194 | 2.8459360 | 0.0125104 | 3 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006574 | 4.10e-05 | 1194 | -16.0492012 | 0.0000000 | 3 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0007740 | 4.10e-05 | 1194 | -18.8951372 | 0.0000000 | 3 |
| AFR | method | Beagle - Eagle | 0 | 0.0004803 | 2.77e-05 | 1194 | 17.3264765 | 0.0000000 | 4 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003427 | 2.77e-05 | 1194 | -12.3642277 | 0.0000000 | 4 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0008230 | 2.77e-05 | 1194 | -29.6907042 | 0.0000000 | 4 |
| AMR | method | Beagle - Eagle | 0 | 0.0000071 | 3.36e-05 | 1194 | 0.2106180 | 0.9758425 | 4 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005188 | 3.36e-05 | 1194 | -15.4513339 | 0.0000000 | 4 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0005258 | 3.36e-05 | 1194 | -15.6619519 | 0.0000000 | 4 |
| EAS | method | Beagle - Eagle | 0 | -0.0003027 | 4.63e-05 | 1194 | -6.5366803 | 0.0000000 | 4 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006647 | 4.63e-05 | 1194 | -14.3531006 | 0.0000000 | 4 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0003620 | 4.63e-05 | 1194 | -7.8164202 | 0.0000000 | 4 |
| EUR | method | Beagle - Eagle | 0 | -0.0000502 | 3.80e-05 | 1194 | -1.3208221 | 0.3838147 | 4 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003238 | 3.80e-05 | 1194 | -8.5229063 | 0.0000000 | 4 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002736 | 3.80e-05 | 1194 | -7.2020843 | 0.0000000 | 4 |
| SAS | method | Beagle - Eagle | 0 | 0.0001167 | 4.26e-05 | 1194 | 2.7371383 | 0.0172855 | 4 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0005308 | 4.26e-05 | 1194 | -12.4524035 | 0.0000000 | 4 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0006474 | 4.26e-05 | 1194 | -15.1895418 | 0.0000000 | 4 |
| AFR | method | Beagle - Eagle | 0 | 0.0005300 | 2.79e-05 | 1194 | 19.0005097 | 0.0000000 | 5 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003829 | 2.79e-05 | 1194 | -13.7265817 | 0.0000000 | 5 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0009129 | 2.79e-05 | 1194 | -32.7270914 | 0.0000000 | 5 |
| AMR | method | Beagle - Eagle | 0 | 0.0000235 | 3.38e-05 | 1194 | 0.6966320 | 0.7655009 | 5 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0006038 | 3.38e-05 | 1194 | -17.8693578 | 0.0000000 | 5 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0006273 | 3.38e-05 | 1194 | -18.5659898 | 0.0000000 | 5 |
| EAS | method | Beagle - Eagle | 0 | -0.0001687 | 4.66e-05 | 1194 | -3.6196228 | 0.0008965 | 5 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006619 | 4.66e-05 | 1194 | -14.2010224 | 0.0000000 | 5 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0004932 | 4.66e-05 | 1194 | -10.5813996 | 0.0000000 | 5 |
| EUR | method | Beagle - Eagle | 0 | -0.0000046 | 3.82e-05 | 1194 | -0.1198941 | 0.9921065 | 5 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003289 | 3.82e-05 | 1194 | -8.6024373 | 0.0000000 | 5 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0003243 | 3.82e-05 | 1194 | -8.4825432 | 0.0000000 | 5 |
| SAS | method | Beagle - Eagle | 0 | 0.0001435 | 4.29e-05 | 1194 | 3.3457221 | 0.0024368 | 5 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006222 | 4.29e-05 | 1194 | -14.5038132 | 0.0000000 | 5 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0007657 | 4.29e-05 | 1194 | -17.8495353 | 0.0000000 | 5 |
| AFR | method | Beagle - Eagle | 0 | 0.0004556 | 2.54e-05 | 1194 | 17.9232098 | 0.0000000 | 6 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003573 | 2.54e-05 | 1194 | -14.0579172 | 0.0000000 | 6 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0008129 | 2.54e-05 | 1194 | -31.9811270 | 0.0000000 | 6 |
| AMR | method | Beagle - Eagle | 0 | 0.0000309 | 3.08e-05 | 1194 | 1.0047598 | 0.5739814 | 6 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0004568 | 3.08e-05 | 1194 | -14.8351085 | 0.0000000 | 6 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0004877 | 3.08e-05 | 1194 | -15.8398683 | 0.0000000 | 6 |
| EAS | method | Beagle - Eagle | 0 | -0.0001687 | 4.25e-05 | 1194 | -3.9722441 | 0.0002226 | 6 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0004946 | 4.25e-05 | 1194 | -11.6451918 | 0.0000000 | 6 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0003259 | 4.25e-05 | 1194 | -7.6729477 | 0.0000000 | 6 |
| EUR | method | Beagle - Eagle | 0 | 0.0000351 | 3.48e-05 | 1194 | 1.0086359 | 0.5715297 | 6 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0002625 | 3.48e-05 | 1194 | -7.5354147 | 0.0000000 | 6 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002977 | 3.48e-05 | 1194 | -8.5440506 | 0.0000000 | 6 |
| SAS | method | Beagle - Eagle | 0 | 0.0001112 | 3.91e-05 | 1194 | 2.8449610 | 0.0125474 | 6 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0005316 | 3.91e-05 | 1194 | -13.5994183 | 0.0000000 | 6 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0006428 | 3.91e-05 | 1194 | -16.4443792 | 0.0000000 | 6 |
| AFR | method | Beagle - Eagle | 0 | 0.0004044 | 2.96e-05 | 1194 | 13.6777630 | 0.0000000 | 7 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004139 | 2.96e-05 | 1194 | -13.9984462 | 0.0000000 | 7 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0008184 | 2.96e-05 | 1194 | -27.6762091 | 0.0000000 | 7 |
| AMR | method | Beagle - Eagle | 0 | 0.0000718 | 3.58e-05 | 1194 | 2.0038332 | 0.1116978 | 7 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0004864 | 3.58e-05 | 1194 | -13.5804758 | 0.0000000 | 7 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0005582 | 3.58e-05 | 1194 | -15.5843090 | 0.0000000 | 7 |
| EAS | method | Beagle - Eagle | 0 | -0.0000917 | 4.94e-05 | 1194 | -1.8552389 | 0.1523649 | 7 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005340 | 4.94e-05 | 1194 | -10.8082895 | 0.0000000 | 7 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0004423 | 4.94e-05 | 1194 | -8.9530505 | 0.0000000 | 7 |
| EUR | method | Beagle - Eagle | 0 | -0.0000572 | 4.05e-05 | 1194 | -1.4112475 | 0.3353662 | 7 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003163 | 4.05e-05 | 1194 | -7.8036290 | 0.0000000 | 7 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002591 | 4.05e-05 | 1194 | -6.3923814 | 0.0000000 | 7 |
| SAS | method | Beagle - Eagle | 0 | 0.0000757 | 4.55e-05 | 1194 | 1.6652420 | 0.2190879 | 7 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006228 | 4.55e-05 | 1194 | -13.6977318 | 0.0000000 | 7 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0006986 | 4.55e-05 | 1194 | -15.3629738 | 0.0000000 | 7 |
| AFR | method | Beagle - Eagle | 0 | 0.0005292 | 3.48e-05 | 1194 | 15.2191879 | 0.0000000 | 8 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004572 | 3.48e-05 | 1194 | -13.1492904 | 0.0000000 | 8 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0009865 | 3.48e-05 | 1194 | -28.3684784 | 0.0000000 | 8 |
| AMR | method | Beagle - Eagle | 0 | -0.0000202 | 4.21e-05 | 1194 | -0.4797532 | 0.8808918 | 8 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0006436 | 4.21e-05 | 1194 | -15.2815689 | 0.0000000 | 8 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0006234 | 4.21e-05 | 1194 | -14.8018156 | 0.0000000 | 8 |
| EAS | method | Beagle - Eagle | 0 | -0.0001358 | 5.81e-05 | 1194 | -2.3378961 | 0.0511116 | 8 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0004508 | 5.81e-05 | 1194 | -7.7595044 | 0.0000000 | 8 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0003150 | 5.81e-05 | 1194 | -5.4216082 | 0.0000002 | 8 |
| EUR | method | Beagle - Eagle | 0 | -0.0000456 | 4.77e-05 | 1194 | -0.9576612 | 0.6038381 | 8 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003383 | 4.77e-05 | 1194 | -7.0978298 | 0.0000000 | 8 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002926 | 4.77e-05 | 1194 | -6.1401686 | 0.0000000 | 8 |
| SAS | method | Beagle - Eagle | 0 | 0.0001073 | 5.35e-05 | 1194 | 2.0074336 | 0.1108289 | 8 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006462 | 5.35e-05 | 1194 | -12.0846881 | 0.0000000 | 8 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0007535 | 5.35e-05 | 1194 | -14.0921217 | 0.0000000 | 8 |
| AFR | method | Beagle - Eagle | 0 | 0.0005048 | 3.23e-05 | 1194 | 15.6450576 | 0.0000000 | 9 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004004 | 3.23e-05 | 1194 | -12.4092070 | 0.0000000 | 9 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0009052 | 3.23e-05 | 1194 | -28.0542646 | 0.0000000 | 9 |
| AMR | method | Beagle - Eagle | 0 | 0.0000480 | 3.91e-05 | 1194 | 1.2283880 | 0.4365983 | 9 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005687 | 3.91e-05 | 1194 | -14.5519496 | 0.0000000 | 9 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0006168 | 3.91e-05 | 1194 | -15.7803376 | 0.0000000 | 9 |
| EAS | method | Beagle - Eagle | 0 | -0.0002605 | 5.39e-05 | 1194 | -4.8323648 | 0.0000046 | 9 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005420 | 5.39e-05 | 1194 | -10.0524216 | 0.0000000 | 9 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0002814 | 5.39e-05 | 1194 | -5.2200568 | 0.0000006 | 9 |
| EUR | method | Beagle - Eagle | 0 | -0.0000072 | 4.42e-05 | 1194 | -0.1623164 | 0.9855803 | 9 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0002646 | 4.42e-05 | 1194 | -5.9827613 | 0.0000000 | 9 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002574 | 4.42e-05 | 1194 | -5.8204448 | 0.0000000 | 9 |
| SAS | method | Beagle - Eagle | 0 | 0.0001511 | 4.96e-05 | 1194 | 3.0445454 | 0.0067259 | 9 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006127 | 4.96e-05 | 1194 | -12.3486181 | 0.0000000 | 9 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0007638 | 4.96e-05 | 1194 | -15.3931635 | 0.0000000 | 9 |
| AFR | method | Beagle - Eagle | 0 | 0.0004400 | 2.97e-05 | 1194 | 14.8217605 | 0.0000000 | 10 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003707 | 2.97e-05 | 1194 | -12.4868312 | 0.0000000 | 10 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0008108 | 2.97e-05 | 1194 | -27.3085918 | 0.0000000 | 10 |
| AMR | method | Beagle - Eagle | 0 | 0.0000027 | 3.60e-05 | 1194 | 0.0763676 | 0.9967899 | 10 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0004847 | 3.60e-05 | 1194 | -13.4772797 | 0.0000000 | 10 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0004874 | 3.60e-05 | 1194 | -13.5536472 | 0.0000000 | 10 |
| EAS | method | Beagle - Eagle | 0 | -0.0002428 | 4.96e-05 | 1194 | -4.8937123 | 0.0000034 | 10 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005918 | 4.96e-05 | 1194 | -11.9304773 | 0.0000000 | 10 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0003491 | 4.96e-05 | 1194 | -7.0367650 | 0.0000000 | 10 |
| EUR | method | Beagle - Eagle | 0 | -0.0000309 | 4.07e-05 | 1194 | -0.7583770 | 0.7286062 | 10 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0002610 | 4.07e-05 | 1194 | -6.4133877 | 0.0000000 | 10 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002301 | 4.07e-05 | 1194 | -5.6550107 | 0.0000001 | 10 |
| SAS | method | Beagle - Eagle | 0 | -0.0000379 | 4.57e-05 | 1194 | -0.8296017 | 0.6846975 | 10 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006058 | 4.57e-05 | 1194 | -13.2696823 | 0.0000000 | 10 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0005679 | 4.57e-05 | 1194 | -12.4400806 | 0.0000000 | 10 |
| AFR | method | Beagle - Eagle | 0 | 0.0004802 | 3.17e-05 | 1194 | 15.1488380 | 0.0000000 | 11 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004014 | 3.17e-05 | 1194 | -12.6630091 | 0.0000000 | 11 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0008817 | 3.17e-05 | 1194 | -27.8118471 | 0.0000000 | 11 |
| AMR | method | Beagle - Eagle | 0 | 0.0000337 | 3.84e-05 | 1194 | 0.8768243 | 0.6550521 | 11 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0004901 | 3.84e-05 | 1194 | -12.7643833 | 0.0000000 | 11 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0005238 | 3.84e-05 | 1194 | -13.6412075 | 0.0000000 | 11 |
| EAS | method | Beagle - Eagle | 0 | -0.0001510 | 5.30e-05 | 1194 | -2.8508519 | 0.0123255 | 11 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005763 | 5.30e-05 | 1194 | -10.8796391 | 0.0000000 | 11 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0004253 | 5.30e-05 | 1194 | -8.0287872 | 0.0000000 | 11 |
| EUR | method | Beagle - Eagle | 0 | -0.0000828 | 4.34e-05 | 1194 | -1.9064647 | 0.1372569 | 11 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0002914 | 4.34e-05 | 1194 | -6.7057425 | 0.0000000 | 11 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002085 | 4.34e-05 | 1194 | -4.7992778 | 0.0000054 | 11 |
| SAS | method | Beagle - Eagle | 0 | 0.0000470 | 4.87e-05 | 1194 | 0.9641536 | 0.5997178 | 11 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0005590 | 4.87e-05 | 1194 | -11.4674726 | 0.0000000 | 11 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0006060 | 4.87e-05 | 1194 | -12.4316263 | 0.0000000 | 11 |
| AFR | method | Beagle - Eagle | 0 | 0.0005216 | 3.93e-05 | 1194 | 13.2622619 | 0.0000000 | 12 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003833 | 3.93e-05 | 1194 | -9.7459948 | 0.0000000 | 12 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0009050 | 3.93e-05 | 1194 | -23.0082566 | 0.0000000 | 12 |
| AMR | method | Beagle - Eagle | 0 | 0.0000017 | 4.76e-05 | 1194 | 0.0347542 | 0.9993343 | 12 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005482 | 4.76e-05 | 1194 | -11.5070928 | 0.0000000 | 12 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0005499 | 4.76e-05 | 1194 | -11.5418470 | 0.0000000 | 12 |
| EAS | method | Beagle - Eagle | 0 | -0.0002102 | 6.57e-05 | 1194 | -3.1985743 | 0.0040464 | 12 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006219 | 6.57e-05 | 1194 | -9.4639273 | 0.0000000 | 12 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0004117 | 6.57e-05 | 1194 | -6.2653530 | 0.0000000 | 12 |
| EUR | method | Beagle - Eagle | 0 | -0.0000254 | 5.39e-05 | 1194 | -0.4711667 | 0.8848616 | 12 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003447 | 5.39e-05 | 1194 | -6.3939818 | 0.0000000 | 12 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0003193 | 5.39e-05 | 1194 | -5.9228152 | 0.0000000 | 12 |
| SAS | method | Beagle - Eagle | 0 | 0.0002536 | 6.05e-05 | 1194 | 4.1928331 | 0.0000877 | 12 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0007569 | 6.05e-05 | 1194 | -12.5137184 | 0.0000000 | 12 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0010105 | 6.05e-05 | 1194 | -16.7065515 | 0.0000000 | 12 |
| AFR | method | Beagle - Eagle | 0 | 0.0005261 | 3.84e-05 | 1194 | 13.6934555 | 0.0000000 | 13 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003936 | 3.84e-05 | 1194 | -10.2447170 | 0.0000000 | 13 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0009197 | 3.84e-05 | 1194 | -23.9381725 | 0.0000000 | 13 |
| AMR | method | Beagle - Eagle | 0 | 0.0000508 | 4.65e-05 | 1194 | 1.0915984 | 0.5194596 | 13 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005557 | 4.65e-05 | 1194 | -11.9413517 | 0.0000000 | 13 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0006065 | 4.65e-05 | 1194 | -13.0329500 | 0.0000000 | 13 |
| EAS | method | Beagle - Eagle | 0 | -0.0002402 | 6.42e-05 | 1194 | -3.7413941 | 0.0005616 | 13 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005023 | 6.42e-05 | 1194 | -7.8252429 | 0.0000000 | 13 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0002622 | 6.42e-05 | 1194 | -4.0838488 | 0.0001397 | 13 |
| EUR | method | Beagle - Eagle | 0 | -0.0000228 | 5.27e-05 | 1194 | -0.4331872 | 0.9017594 | 13 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0002979 | 5.27e-05 | 1194 | -5.6572024 | 0.0000001 | 13 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002751 | 5.27e-05 | 1194 | -5.2240152 | 0.0000006 | 13 |
| SAS | method | Beagle - Eagle | 0 | -0.0002002 | 5.91e-05 | 1194 | -3.3883083 | 0.0020959 | 13 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0007263 | 5.91e-05 | 1194 | -12.2937546 | 0.0000000 | 13 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0005262 | 5.91e-05 | 1194 | -8.9054463 | 0.0000000 | 13 |
| AFR | method | Beagle - Eagle | 0 | 0.0004452 | 3.62e-05 | 1194 | 12.3085578 | 0.0000000 | 14 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004266 | 3.62e-05 | 1194 | -11.7920322 | 0.0000000 | 14 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0008718 | 3.62e-05 | 1194 | -24.1005900 | 0.0000000 | 14 |
| AMR | method | Beagle - Eagle | 0 | -0.0000236 | 4.38e-05 | 1194 | -0.5377136 | 0.8527486 | 14 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005755 | 4.38e-05 | 1194 | -13.1343977 | 0.0000000 | 14 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0005519 | 4.38e-05 | 1194 | -12.5966841 | 0.0000000 | 14 |
| EAS | method | Beagle - Eagle | 0 | -0.0004212 | 6.04e-05 | 1194 | -6.9683875 | 0.0000000 | 14 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006728 | 6.04e-05 | 1194 | -11.1314465 | 0.0000000 | 14 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0002516 | 6.04e-05 | 1194 | -4.1630590 | 0.0000997 | 14 |
| EUR | method | Beagle - Eagle | 0 | -0.0001347 | 4.96e-05 | 1194 | -2.7177888 | 0.0182858 | 14 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0004064 | 4.96e-05 | 1194 | -8.1964235 | 0.0000000 | 14 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002716 | 4.96e-05 | 1194 | -5.4786347 | 0.0000002 | 14 |
| SAS | method | Beagle - Eagle | 0 | 0.0000396 | 5.56e-05 | 1194 | 0.7124864 | 0.7561536 | 14 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006810 | 5.56e-05 | 1194 | -12.2420022 | 0.0000000 | 14 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0007206 | 5.56e-05 | 1194 | -12.9544886 | 0.0000000 | 14 |
| AFR | method | Beagle - Eagle | 0 | 0.0003587 | 3.80e-05 | 1194 | 9.4386505 | 0.0000000 | 15 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003949 | 3.80e-05 | 1194 | -10.3903120 | 0.0000000 | 15 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0007536 | 3.80e-05 | 1194 | -19.8289624 | 0.0000000 | 15 |
| AMR | method | Beagle - Eagle | 0 | -0.0000228 | 4.60e-05 | 1194 | -0.4962488 | 0.8731169 | 15 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0006085 | 4.60e-05 | 1194 | -13.2192618 | 0.0000000 | 15 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0005857 | 4.60e-05 | 1194 | -12.7230130 | 0.0000000 | 15 |
| EAS | method | Beagle - Eagle | 0 | -0.0002662 | 6.35e-05 | 1194 | -4.1924257 | 0.0000878 | 15 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006438 | 6.35e-05 | 1194 | -10.1394519 | 0.0000000 | 15 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0003776 | 6.35e-05 | 1194 | -5.9470262 | 0.0000000 | 15 |
| EUR | method | Beagle - Eagle | 0 | -0.0000594 | 5.21e-05 | 1194 | -1.1409907 | 0.4890059 | 15 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003142 | 5.21e-05 | 1194 | -6.0314706 | 0.0000000 | 15 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002547 | 5.21e-05 | 1194 | -4.8904799 | 0.0000034 | 15 |
| SAS | method | Beagle - Eagle | 0 | -0.0001424 | 5.84e-05 | 1194 | -2.4374077 | 0.0396042 | 15 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0008296 | 5.84e-05 | 1194 | -14.1949264 | 0.0000000 | 15 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0006871 | 5.84e-05 | 1194 | -11.7575187 | 0.0000000 | 15 |
| AFR | method | Beagle - Eagle | 0 | 0.0003689 | 4.77e-05 | 1194 | 7.7338629 | 0.0000000 | 16 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003993 | 4.77e-05 | 1194 | -8.3715322 | 0.0000000 | 16 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0007682 | 4.77e-05 | 1194 | -16.1053950 | 0.0000000 | 16 |
| AMR | method | Beagle - Eagle | 0 | 0.0000565 | 5.78e-05 | 1194 | 0.9779683 | 0.5909538 | 16 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0006281 | 5.78e-05 | 1194 | -10.8712620 | 0.0000000 | 16 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0006846 | 5.78e-05 | 1194 | -11.8492303 | 0.0000000 | 16 |
| EAS | method | Beagle - Eagle | 0 | -0.0002005 | 7.97e-05 | 1194 | -2.5156145 | 0.0321812 | 16 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006164 | 7.97e-05 | 1194 | -7.7342443 | 0.0000000 | 16 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0004159 | 7.97e-05 | 1194 | -5.2186298 | 0.0000006 | 16 |
| EUR | method | Beagle - Eagle | 0 | -0.0002904 | 6.54e-05 | 1194 | -4.4419836 | 0.0000290 | 16 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0006080 | 6.54e-05 | 1194 | -9.2998373 | 0.0000000 | 16 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0003176 | 6.54e-05 | 1194 | -4.8578538 | 0.0000040 | 16 |
| SAS | method | Beagle - Eagle | 0 | 0.0004022 | 7.33e-05 | 1194 | 5.4832923 | 0.0000002 | 16 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0005987 | 7.33e-05 | 1194 | -8.1627773 | 0.0000000 | 16 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0010009 | 7.33e-05 | 1194 | -13.6460695 | 0.0000000 | 16 |
| AFR | method | Beagle - Eagle | 0 | 0.0002622 | 4.38e-05 | 1194 | 5.9858512 | 0.0000000 | 17 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004987 | 4.38e-05 | 1194 | -11.3826610 | 0.0000000 | 17 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0007609 | 4.38e-05 | 1194 | -17.3685122 | 0.0000000 | 17 |
| AMR | method | Beagle - Eagle | 0 | -0.0000364 | 5.31e-05 | 1194 | -0.6852430 | 0.7721556 | 17 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005208 | 5.31e-05 | 1194 | -9.8149434 | 0.0000000 | 17 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0004845 | 5.31e-05 | 1194 | -9.1297004 | 0.0000000 | 17 |
| EAS | method | Beagle - Eagle | 0 | -0.0002022 | 7.32e-05 | 1194 | -2.7617166 | 0.0160847 | 17 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005352 | 7.32e-05 | 1194 | -7.3110209 | 0.0000000 | 17 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0003330 | 7.32e-05 | 1194 | -4.5493043 | 0.0000177 | 17 |
| EUR | method | Beagle - Eagle | 0 | -0.0001355 | 6.00e-05 | 1194 | -2.2565365 | 0.0624910 | 17 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003435 | 6.00e-05 | 1194 | -5.7210562 | 0.0000000 | 17 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002080 | 6.00e-05 | 1194 | -3.4645197 | 0.0015934 | 17 |
| SAS | method | Beagle - Eagle | 0 | -0.0001435 | 6.74e-05 | 1194 | -2.1304709 | 0.0841853 | 17 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006087 | 6.74e-05 | 1194 | -9.0352654 | 0.0000000 | 17 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0004652 | 6.74e-05 | 1194 | -6.9047945 | 0.0000000 | 17 |
| AFR | method | Beagle - Eagle | 0 | 0.0004286 | 3.54e-05 | 1194 | 12.1029163 | 0.0000000 | 18 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004583 | 3.54e-05 | 1194 | -12.9413121 | 0.0000000 | 18 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0008869 | 3.54e-05 | 1194 | -25.0442284 | 0.0000000 | 18 |
| AMR | method | Beagle - Eagle | 0 | 0.0000538 | 4.29e-05 | 1194 | 1.2552844 | 0.4209309 | 18 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005582 | 4.29e-05 | 1194 | -13.0135443 | 0.0000000 | 18 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0006121 | 4.29e-05 | 1194 | -14.2688287 | 0.0000000 | 18 |
| EAS | method | Beagle - Eagle | 0 | -0.0002549 | 5.92e-05 | 1194 | -4.3080744 | 0.0000529 | 18 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005295 | 5.92e-05 | 1194 | -8.9482588 | 0.0000000 | 18 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0002746 | 5.92e-05 | 1194 | -4.6401844 | 0.0000115 | 18 |
| EUR | method | Beagle - Eagle | 0 | -0.0001363 | 4.85e-05 | 1194 | -2.8088141 | 0.0139881 | 18 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003425 | 4.85e-05 | 1194 | -7.0553912 | 0.0000000 | 18 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002061 | 4.85e-05 | 1194 | -4.2465772 | 0.0000694 | 18 |
| SAS | method | Beagle - Eagle | 0 | 0.0000726 | 5.45e-05 | 1194 | 1.3331711 | 0.3770016 | 18 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006050 | 5.45e-05 | 1194 | -11.1083313 | 0.0000000 | 18 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0006776 | 5.45e-05 | 1194 | -12.4415024 | 0.0000000 | 18 |
| AFR | method | Beagle - Eagle | 0 | 0.0003216 | 4.30e-05 | 1194 | 7.4813169 | 0.0000000 | 19 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003063 | 4.30e-05 | 1194 | -7.1249908 | 0.0000000 | 19 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0006280 | 4.30e-05 | 1194 | -14.6063077 | 0.0000000 | 19 |
| AMR | method | Beagle - Eagle | 0 | -0.0000811 | 5.21e-05 | 1194 | -1.5577378 | 0.2645574 | 19 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0004183 | 5.21e-05 | 1194 | -8.0328288 | 0.0000000 | 19 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0003372 | 5.21e-05 | 1194 | -6.4750909 | 0.0000000 | 19 |
| EAS | method | Beagle - Eagle | 0 | -0.0001522 | 7.18e-05 | 1194 | -2.1189795 | 0.0864328 | 19 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005116 | 7.18e-05 | 1194 | -7.1215054 | 0.0000000 | 19 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0003593 | 7.18e-05 | 1194 | -5.0025259 | 0.0000019 | 19 |
| EUR | method | Beagle - Eagle | 0 | -0.0000906 | 5.89e-05 | 1194 | -1.5378709 | 0.2735718 | 19 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0002416 | 5.89e-05 | 1194 | -4.1009873 | 0.0001299 | 19 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0001510 | 5.89e-05 | 1194 | -2.5631163 | 0.0282837 | 19 |
| SAS | method | Beagle - Eagle | 0 | 0.0000927 | 6.61e-05 | 1194 | 1.4019229 | 0.3402032 | 19 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006045 | 6.61e-05 | 1194 | -9.1442675 | 0.0000000 | 19 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0006972 | 6.61e-05 | 1194 | -10.5461904 | 0.0000000 | 19 |
| AFR | method | Beagle - Eagle | 0 | 0.0003607 | 4.12e-05 | 1194 | 8.7486537 | 0.0000000 | 20 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003029 | 4.12e-05 | 1194 | -7.3462005 | 0.0000000 | 20 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0006636 | 4.12e-05 | 1194 | -16.0948542 | 0.0000000 | 20 |
| AMR | method | Beagle - Eagle | 0 | -0.0000567 | 4.99e-05 | 1194 | -1.1358979 | 0.4921217 | 20 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005121 | 4.99e-05 | 1194 | -10.2540553 | 0.0000000 | 20 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0004554 | 4.99e-05 | 1194 | -9.1181574 | 0.0000000 | 20 |
| EAS | method | Beagle - Eagle | 0 | -0.0002879 | 6.89e-05 | 1194 | -4.1788964 | 0.0000931 | 20 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005742 | 6.89e-05 | 1194 | -8.3355057 | 0.0000000 | 20 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0002863 | 6.89e-05 | 1194 | -4.1566093 | 0.0001025 | 20 |
| EUR | method | Beagle - Eagle | 0 | -0.0001733 | 5.65e-05 | 1194 | -3.0673045 | 0.0062486 | 20 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003020 | 5.65e-05 | 1194 | -5.3445971 | 0.0000003 | 20 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0001287 | 5.65e-05 | 1194 | -2.2772926 | 0.0594055 | 20 |
| SAS | method | Beagle - Eagle | 0 | 0.0000269 | 6.34e-05 | 1194 | 0.4249621 | 0.9052721 | 20 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0005352 | 6.34e-05 | 1194 | -8.4418609 | 0.0000000 | 20 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0005622 | 6.34e-05 | 1194 | -8.8668230 | 0.0000000 | 20 |
| AFR | method | Beagle - Eagle | 0 | 0.0003008 | 4.79e-05 | 1194 | 6.2726141 | 0.0000000 | 21 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004479 | 4.79e-05 | 1194 | -9.3411600 | 0.0000000 | 21 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0007487 | 4.79e-05 | 1194 | -15.6137740 | 0.0000000 | 21 |
| AMR | method | Beagle - Eagle | 0 | -0.0001152 | 5.81e-05 | 1194 | -1.9843647 | 0.1164881 | 21 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0006034 | 5.81e-05 | 1194 | -10.3886910 | 0.0000000 | 21 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0004881 | 5.81e-05 | 1194 | -8.4043262 | 0.0000000 | 21 |
| EAS | method | Beagle - Eagle | 0 | -0.0002090 | 8.01e-05 | 1194 | -2.6088978 | 0.0249208 | 21 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0004776 | 8.01e-05 | 1194 | -5.9608976 | 0.0000000 | 21 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0002685 | 8.01e-05 | 1194 | -3.3519998 | 0.0023836 | 21 |
| EUR | method | Beagle - Eagle | 0 | -0.0001388 | 6.57e-05 | 1194 | -2.1114952 | 0.0879222 | 21 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0004037 | 6.57e-05 | 1194 | -6.1423595 | 0.0000000 | 21 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0002649 | 6.57e-05 | 1194 | -4.0308643 | 0.0001745 | 21 |
| SAS | method | Beagle - Eagle | 0 | -0.0000789 | 7.37e-05 | 1194 | -1.0696380 | 0.5331493 | 21 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006798 | 7.37e-05 | 1194 | -9.2191316 | 0.0000000 | 21 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0006009 | 7.37e-05 | 1194 | -8.1494936 | 0.0000000 | 21 |
| AFR | method | Beagle - Eagle | 0 | 0.0001776 | 5.35e-05 | 1194 | 3.3221526 | 0.0026468 | 22 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003215 | 5.35e-05 | 1194 | -6.0125758 | 0.0000000 | 22 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0004991 | 5.35e-05 | 1194 | -9.3347284 | 0.0000000 | 22 |
| AMR | method | Beagle - Eagle | 0 | -0.0001744 | 6.48e-05 | 1194 | -2.6923316 | 0.0196794 | 22 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0004658 | 6.48e-05 | 1194 | -7.1925821 | 0.0000000 | 22 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0002914 | 6.48e-05 | 1194 | -4.5002504 | 0.0000222 | 22 |
| EAS | method | Beagle - Eagle | 0 | -0.0004043 | 8.93e-05 | 1194 | -4.5254701 | 0.0000197 | 22 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0004010 | 8.93e-05 | 1194 | -4.4883624 | 0.0000234 | 22 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0000033 | 8.93e-05 | 1194 | 0.0371077 | 0.9992411 | 22 |
| EUR | method | Beagle - Eagle | 0 | -0.0001993 | 7.33e-05 | 1194 | -2.7191826 | 0.0182121 | 22 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003548 | 7.33e-05 | 1194 | -4.8410279 | 0.0000044 | 22 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0001555 | 7.33e-05 | 1194 | -2.1218453 | 0.0858678 | 22 |
| SAS | method | Beagle - Eagle | 0 | -0.0001315 | 8.22e-05 | 1194 | -1.5988523 | 0.2465055 | 22 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006356 | 8.22e-05 | 1194 | -7.7299990 | 0.0000000 | 22 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0005041 | 8.22e-05 | 1194 | -6.1311467 | 0.0000000 | 22 |
| AFR | method | Beagle - Eagle | 0 | -0.0004588 | 1.80e-05 | 1990 | -25.4372255 | 0.0000000 | 23 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0000692 | 1.80e-05 | 1990 | -3.8350570 | 0.0003805 | 23 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0003896 | 1.80e-05 | 1990 | 21.6021685 | 0.0000000 | 23 |
| AMR | method | Beagle - Eagle | 0 | -0.0004346 | 1.80e-05 | 1990 | -24.0941650 | 0.0000000 | 23 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000927 | 1.80e-05 | 1990 | -5.1416197 | 0.0000009 | 23 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0003418 | 1.80e-05 | 1990 | 18.9525452 | 0.0000000 | 23 |
| EAS | method | Beagle - Eagle | 0 | -0.0008134 | 1.80e-05 | 1990 | -45.0949894 | 0.0000000 | 23 |
| EAS | method | Beagle - SHAPEIT | 0 | 0.0000256 | 1.80e-05 | 1990 | 1.4204075 | 0.3305162 | 23 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008390 | 1.80e-05 | 1990 | 46.5153968 | 0.0000000 | 23 |
| EUR | method | Beagle - Eagle | 0 | -0.0005408 | 1.80e-05 | 1990 | -29.9828894 | 0.0000000 | 23 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0000649 | 1.80e-05 | 1990 | -3.5966972 | 0.0009624 | 23 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0004759 | 1.80e-05 | 1990 | 26.3861922 | 0.0000000 | 23 |
| SAS | method | Beagle - Eagle | 0 | -0.0006780 | 1.80e-05 | 1990 | -37.5903655 | 0.0000000 | 23 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0000273 | 1.80e-05 | 1990 | -1.5111478 | 0.2858440 | 23 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0006508 | 1.80e-05 | 1990 | 36.0792178 | 0.0000000 | 23 |
df_pop_pop %>% knitr::kable()
| method | term | contrast | null.value | estimate | std.error | df | statistic | adj.p.value | chrom |
|---|---|---|---|---|---|---|---|---|---|
| Beagle | SUPER | AFR - AMR | 0 | -0.0012125 | 0.0001918 | 616.1882 | -6.3226634 | 0.0000000 | 1 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0045375 | 0.0002377 | 616.1882 | -19.0863327 | 0.0000000 | 1 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0010421 | 0.0002071 | 616.1882 | -5.0308144 | 0.0000064 | 1 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0034997 | 0.0002240 | 616.1882 | -15.6273412 | 0.0000000 | 1 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0033250 | 0.0002520 | 616.1882 | -13.1968292 | 0.0000000 | 1 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001704 | 0.0002233 | 616.1882 | 0.7630794 | 0.9410205 | 1 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0022873 | 0.0002390 | 616.1882 | -9.5704702 | 0.0000000 | 1 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0034954 | 0.0002638 | 616.1882 | 13.2481109 | 0.0000000 | 1 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0010377 | 0.0002772 | 616.1882 | 3.7431667 | 0.0018528 | 1 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0024577 | 0.0002515 | 616.1882 | -9.7723339 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0016806 | 0.0001918 | 616.1882 | -8.7639580 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0052678 | 0.0002377 | 616.1882 | -22.1580917 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0015956 | 0.0002071 | 616.1882 | -7.7030756 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0039263 | 0.0002240 | 616.1882 | -17.5320761 | 0.0000000 | 1 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0035871 | 0.0002520 | 616.1882 | -14.2371048 | 0.0000000 | 1 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000850 | 0.0002233 | 616.1882 | 0.3808090 | 0.9955331 | 1 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0022457 | 0.0002390 | 616.1882 | -9.3964212 | 0.0000000 | 1 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0036721 | 0.0002638 | 616.1882 | 13.9179639 | 0.0000000 | 1 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0013414 | 0.0002772 | 616.1882 | 4.8386172 | 0.0000163 | 1 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0023307 | 0.0002515 | 616.1882 | -9.2674955 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0013815 | 0.0001918 | 616.1882 | -7.2039711 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0047098 | 0.0002377 | 616.1882 | -19.8111881 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0009697 | 0.0002071 | 616.1882 | -4.6811806 | 0.0000345 | 1 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0037750 | 0.0002240 | 616.1882 | -16.8565374 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0033283 | 0.0002520 | 616.1882 | -13.2099938 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004118 | 0.0002233 | 616.1882 | 1.8441927 | 0.3491025 | 1 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0023935 | 0.0002390 | 616.1882 | -10.0151392 | 0.0000000 | 1 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0037402 | 0.0002638 | 616.1882 | 14.1757339 | 0.0000000 | 1 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0009348 | 0.0002772 | 616.1882 | 3.3718037 | 0.0070774 | 1 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0028054 | 0.0002515 | 616.1882 | -11.1548852 | 0.0000000 | 1 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0014510 | 0.0001893 | 618.2141 | -7.6661287 | 0.0000000 | 2 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0045791 | 0.0002346 | 618.2141 | -19.5149909 | 0.0000000 | 2 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0008447 | 0.0002044 | 618.2141 | -4.1317571 | 0.0003933 | 2 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0035259 | 0.0002210 | 618.2141 | -15.9513954 | 0.0000000 | 2 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0031281 | 0.0002487 | 618.2141 | -12.5787557 | 0.0000000 | 2 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0006063 | 0.0002204 | 618.2141 | 2.7506861 | 0.0480162 | 2 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0020749 | 0.0002359 | 618.2141 | -8.7961269 | 0.0000000 | 2 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0037344 | 0.0002604 | 618.2141 | 14.3401901 | 0.0000000 | 2 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0010532 | 0.0002736 | 618.2141 | 3.8489790 | 0.0012325 | 2 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0026812 | 0.0002482 | 618.2141 | -10.8013964 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0018796 | 0.0001893 | 618.2141 | -9.9307186 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0052680 | 0.0002346 | 618.2141 | -22.4507941 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0013335 | 0.0002044 | 618.2141 | -6.5223458 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0038909 | 0.0002210 | 618.2141 | -17.6026197 | 0.0000000 | 2 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0033883 | 0.0002487 | 618.2141 | -13.6252422 | 0.0000000 | 2 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0005462 | 0.0002204 | 618.2141 | 2.4779423 | 0.0969742 | 2 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0020112 | 0.0002359 | 618.2141 | -8.5263112 | 0.0000000 | 2 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0039345 | 0.0002604 | 618.2141 | 15.1086773 | 0.0000000 | 2 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0013771 | 0.0002736 | 618.2141 | 5.0326298 | 0.0000063 | 2 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0025574 | 0.0002482 | 618.2141 | -10.3028069 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0015523 | 0.0001893 | 618.2141 | -8.2014905 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0048366 | 0.0002346 | 618.2141 | -20.6124634 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0007976 | 0.0002044 | 618.2141 | -3.9013075 | 0.0010036 | 2 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0037531 | 0.0002210 | 618.2141 | -16.9793542 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0032843 | 0.0002487 | 618.2141 | -13.2068142 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0007547 | 0.0002204 | 618.2141 | 3.4241741 | 0.0059079 | 2 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0022008 | 0.0002359 | 618.2141 | -9.3298123 | 0.0000000 | 2 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0040390 | 0.0002604 | 618.2141 | 15.5099899 | 0.0000000 | 2 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0010835 | 0.0002736 | 618.2141 | 3.9597004 | 0.0007954 | 2 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0029555 | 0.0002482 | 618.2141 | -11.9065845 | 0.0000000 | 2 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0012736 | 0.0001824 | 618.4175 | -6.9842973 | 0.0000000 | 3 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0042897 | 0.0002261 | 618.4175 | -18.9757873 | 0.0000000 | 3 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0010075 | 0.0001970 | 618.4175 | -5.1150992 | 0.0000042 | 3 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0032765 | 0.0002130 | 618.4175 | -15.3859277 | 0.0000000 | 3 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0030161 | 0.0002396 | 618.4175 | -12.5889395 | 0.0000000 | 3 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0002661 | 0.0002124 | 618.4175 | 1.2530659 | 0.7200460 | 3 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0020029 | 0.0002273 | 618.4175 | -8.8133525 | 0.0000000 | 3 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0032822 | 0.0002509 | 618.4175 | 13.0823331 | 0.0000000 | 3 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0010132 | 0.0002636 | 618.4175 | 3.8433848 | 0.0012597 | 3 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0022690 | 0.0002391 | 618.4175 | -9.4879388 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0017058 | 0.0001824 | 618.4175 | -9.3546293 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0050098 | 0.0002261 | 618.4175 | -22.1612288 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0015409 | 0.0001970 | 618.4175 | -7.8228288 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0036619 | 0.0002130 | 618.4175 | -17.1955558 | 0.0000000 | 3 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0033040 | 0.0002396 | 618.4175 | -13.7904928 | 0.0000000 | 3 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0001650 | 0.0002124 | 618.4175 | 0.7769585 | 0.9372165 | 3 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0019560 | 0.0002273 | 618.4175 | -8.6071232 | 0.0000000 | 3 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0034690 | 0.0002509 | 618.4175 | 13.8267740 | 0.0000000 | 3 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0013479 | 0.0002636 | 618.4175 | 5.1131469 | 0.0000042 | 3 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0021210 | 0.0002391 | 618.4175 | -8.8691961 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0013764 | 0.0001824 | 618.4175 | -7.5481042 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0044414 | 0.0002261 | 618.4175 | -19.6467338 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0009338 | 0.0001970 | 618.4175 | -4.7407509 | 0.0000260 | 3 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0035155 | 0.0002130 | 618.4175 | -16.5081940 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0030650 | 0.0002396 | 618.4175 | -12.7928942 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004426 | 0.0002124 | 618.4175 | 2.0844555 | 0.2280753 | 3 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0021391 | 0.0002273 | 618.4175 | -9.4125857 | 0.0000000 | 3 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0035076 | 0.0002509 | 618.4175 | 13.9807848 | 0.0000000 | 3 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0009259 | 0.0002636 | 618.4175 | 3.5121715 | 0.0043348 | 3 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0025817 | 0.0002391 | 618.4175 | -10.7956267 | 0.0000000 | 3 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0014318 | 0.0001666 | 624.9824 | -8.5965559 | 0.0000000 | 4 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0037890 | 0.0002065 | 624.9824 | -18.3502878 | 0.0000000 | 4 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0009205 | 0.0001799 | 624.9824 | -5.1164543 | 0.0000041 | 4 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0032001 | 0.0001945 | 624.9824 | -16.4523674 | 0.0000000 | 4 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0023572 | 0.0002188 | 624.9824 | -10.7716189 | 0.0000000 | 4 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0005113 | 0.0001940 | 624.9824 | 2.6363058 | 0.0651550 | 4 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0017683 | 0.0002076 | 624.9824 | -8.5189904 | 0.0000000 | 4 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0028685 | 0.0002292 | 624.9824 | 12.5176632 | 0.0000000 | 4 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005889 | 0.0002408 | 624.9824 | 2.4455429 | 0.1047865 | 4 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0022796 | 0.0002184 | 624.9824 | -10.4364704 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0019050 | 0.0001666 | 624.9824 | -11.4375177 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0045719 | 0.0002065 | 624.9824 | -22.1423035 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0014509 | 0.0001799 | 624.9824 | -8.0648147 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0035637 | 0.0001945 | 624.9824 | -18.3216285 | 0.0000000 | 4 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0026670 | 0.0002188 | 624.9824 | -12.1873065 | 0.0000000 | 4 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0004541 | 0.0001940 | 624.9824 | 2.3411432 | 0.1334060 | 4 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0016587 | 0.0002076 | 624.9824 | -7.9910055 | 0.0000000 | 4 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0031210 | 0.0002292 | 624.9824 | 13.6197417 | 0.0000000 | 4 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0010082 | 0.0002408 | 624.9824 | 4.1872818 | 0.0003111 | 4 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0021128 | 0.0002184 | 624.9824 | -9.6726375 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0016079 | 0.0001666 | 624.9824 | -9.6535308 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0041110 | 0.0002065 | 624.9824 | -19.9097927 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0009016 | 0.0001799 | 624.9824 | -5.0112483 | 0.0000070 | 4 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0033882 | 0.0001945 | 624.9824 | -17.4191854 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0025031 | 0.0002188 | 624.9824 | -11.4386233 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0007063 | 0.0001940 | 624.9824 | 3.6415483 | 0.0027082 | 4 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0017803 | 0.0002076 | 624.9824 | -8.5768384 | 0.0000000 | 4 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0032094 | 0.0002292 | 624.9824 | 14.0054502 | 0.0000000 | 4 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0007228 | 0.0002408 | 624.9824 | 3.0018544 | 0.0232890 | 4 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0024866 | 0.0002184 | 624.9824 | -11.3840583 | 0.0000000 | 4 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0011335 | 0.0001901 | 618.6204 | -5.9628756 | 0.0000000 | 5 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0042093 | 0.0002357 | 618.6204 | -17.8622579 | 0.0000000 | 5 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0008796 | 0.0002053 | 618.6204 | -4.2837826 | 0.0002062 | 5 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0034256 | 0.0002220 | 618.6204 | -15.4310327 | 0.0000000 | 5 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0030759 | 0.0002498 | 618.6204 | -12.3156806 | 0.0000000 | 5 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0002539 | 0.0002214 | 618.6204 | 1.1470363 | 0.7813251 | 5 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0022921 | 0.0002369 | 618.6204 | -9.6752120 | 0.0000000 | 5 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0033298 | 0.0002615 | 618.6204 | 12.7316428 | 0.0000000 | 5 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0007838 | 0.0002748 | 618.6204 | 2.8520784 | 0.0361675 | 5 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0025460 | 0.0002493 | 618.6204 | -10.2128077 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0016400 | 0.0001901 | 618.6204 | -8.6273259 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0049081 | 0.0002357 | 618.6204 | -20.8273037 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0014142 | 0.0002053 | 618.6204 | -6.8874783 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0038121 | 0.0002220 | 618.6204 | -17.1721184 | 0.0000000 | 5 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0032681 | 0.0002498 | 618.6204 | -13.0854173 | 0.0000000 | 5 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002258 | 0.0002214 | 618.6204 | 1.0199953 | 0.8461585 | 5 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0021721 | 0.0002369 | 618.6204 | -9.1687524 | 0.0000000 | 5 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0034939 | 0.0002615 | 618.6204 | 13.3591717 | 0.0000000 | 5 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0010960 | 0.0002748 | 618.6204 | 3.9882156 | 0.0007091 | 5 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0023979 | 0.0002493 | 618.6204 | -9.6187154 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0013544 | 0.0001901 | 618.6204 | -7.1248035 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0044883 | 0.0002357 | 618.6204 | -19.0460952 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0008256 | 0.0002053 | 618.6204 | -4.0207336 | 0.0006216 | 5 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0036648 | 0.0002220 | 618.6204 | -16.5087887 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0031340 | 0.0002498 | 618.6204 | -12.5483373 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0005288 | 0.0002214 | 618.6204 | 2.3888142 | 0.1196902 | 5 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0023104 | 0.0002369 | 618.6204 | -9.7528012 | 0.0000000 | 5 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0036627 | 0.0002615 | 618.6204 | 14.0048548 | 0.0000000 | 5 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0008235 | 0.0002748 | 618.6204 | 2.9966330 | 0.0236668 | 5 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0028392 | 0.0002493 | 618.6204 | -11.3891895 | 0.0000000 | 5 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0010278 | 0.0001689 | 619.7714 | -6.0861081 | 0.0000000 | 6 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0036264 | 0.0002094 | 619.7714 | -17.3206822 | 0.0000000 | 6 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0006144 | 0.0001824 | 619.7714 | -3.3679924 | 0.0071679 | 6 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0029280 | 0.0001972 | 619.7714 | -14.8459920 | 0.0000000 | 6 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0025985 | 0.0002219 | 619.7714 | -11.7108756 | 0.0000000 | 6 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0004135 | 0.0001967 | 619.7714 | 2.1023116 | 0.2203142 | 6 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0019002 | 0.0002105 | 619.7714 | -9.0281098 | 0.0000000 | 6 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0030120 | 0.0002324 | 619.7714 | 12.9626300 | 0.0000000 | 6 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0006983 | 0.0002442 | 619.7714 | 2.8602610 | 0.0353300 | 6 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0023136 | 0.0002215 | 619.7714 | -10.4461174 | 0.0000000 | 6 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0014525 | 0.0001689 | 619.7714 | -8.6006535 | 0.0000000 | 6 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0042507 | 0.0002094 | 619.7714 | -20.3026035 | 0.0000000 | 6 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0010349 | 0.0001824 | 619.7714 | -5.6728974 | 0.0000002 | 6 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0032724 | 0.0001972 | 619.7714 | -16.5921877 | 0.0000000 | 6 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0027982 | 0.0002219 | 619.7714 | -12.6106311 | 0.0000000 | 6 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0004177 | 0.0001967 | 619.7714 | 2.1236894 | 0.2112593 | 6 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0018199 | 0.0002105 | 619.7714 | -8.6467229 | 0.0000000 | 6 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0032158 | 0.0002324 | 619.7714 | 13.8399410 | 0.0000000 | 6 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0009783 | 0.0002442 | 619.7714 | 4.0067414 | 0.0006578 | 6 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0022376 | 0.0002215 | 619.7714 | -10.1026708 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0011273 | 0.0001689 | 619.7714 | -6.6748165 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0037636 | 0.0002094 | 619.7714 | -17.9762149 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0005196 | 0.0001824 | 619.7714 | -2.8482309 | 0.0365645 | 6 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0031023 | 0.0001972 | 619.7714 | -15.7294721 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0026363 | 0.0002219 | 619.7714 | -11.8813333 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0006077 | 0.0001967 | 619.7714 | 3.0899647 | 0.0177762 | 6 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0019750 | 0.0002105 | 619.7714 | -9.3836041 | 0.0000000 | 6 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0032440 | 0.0002324 | 619.7714 | 13.9613549 | 0.0000000 | 6 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0006613 | 0.0002442 | 619.7714 | 2.7087206 | 0.0538020 | 6 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0025827 | 0.0002215 | 619.7714 | -11.6609377 | 0.0000000 | 6 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0011244 | 0.0001844 | 622.9174 | -6.0965236 | 0.0000000 | 7 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0042376 | 0.0002286 | 622.9174 | -18.5336840 | 0.0000000 | 7 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0006582 | 0.0001992 | 622.9174 | -3.3037046 | 0.0089057 | 7 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0032267 | 0.0002154 | 622.9174 | -14.9807430 | 0.0000000 | 7 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0031132 | 0.0002423 | 622.9174 | -12.8474905 | 0.0000000 | 7 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0004663 | 0.0002148 | 622.9174 | 2.1708866 | 0.1921619 | 7 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0021022 | 0.0002299 | 622.9174 | -9.1460225 | 0.0000000 | 7 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0035795 | 0.0002538 | 622.9174 | 14.1060761 | 0.0000000 | 7 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0010110 | 0.0002666 | 622.9174 | 3.7915799 | 0.0015384 | 7 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0025685 | 0.0002419 | 622.9174 | -10.6190609 | 0.0000000 | 7 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0014571 | 0.0001844 | 622.9174 | -7.9002640 | 0.0000000 | 7 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0047337 | 0.0002286 | 622.9174 | -20.7034351 | 0.0000000 | 7 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0011198 | 0.0001992 | 622.9174 | -5.6209473 | 0.0000003 | 7 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0035554 | 0.0002154 | 622.9174 | -16.5069426 | 0.0000000 | 7 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0032766 | 0.0002423 | 622.9174 | -13.5219213 | 0.0000000 | 7 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003373 | 0.0002148 | 622.9174 | 1.5704299 | 0.5170067 | 7 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0020983 | 0.0002299 | 622.9174 | -9.1288384 | 0.0000000 | 7 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0036139 | 0.0002538 | 622.9174 | 14.2418953 | 0.0000000 | 7 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0011784 | 0.0002666 | 622.9174 | 4.4193220 | 0.0001137 | 7 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0024356 | 0.0002419 | 622.9174 | -10.0695494 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0011969 | 0.0001844 | 622.9174 | -6.4894864 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0043577 | 0.0002286 | 622.9174 | -19.0587872 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0005605 | 0.0001992 | 622.9174 | -2.8134642 | 0.0403378 | 7 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0034356 | 0.0002154 | 622.9174 | -15.9507131 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0031608 | 0.0002423 | 622.9174 | -13.0438658 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0006364 | 0.0002148 | 622.9174 | 2.9630642 | 0.0261650 | 7 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0022387 | 0.0002299 | 622.9174 | -9.7396305 | 0.0000000 | 7 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0037972 | 0.0002538 | 622.9174 | 14.9641009 | 0.0000000 | 7 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0009221 | 0.0002666 | 622.9174 | 3.4583276 | 0.0052416 | 7 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0028751 | 0.0002419 | 622.9174 | -11.8865845 | 0.0000000 | 7 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0014515 | 0.0001926 | 630.1012 | -7.5359547 | 0.0000000 | 8 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0046079 | 0.0002388 | 630.1012 | -19.2983258 | 0.0000000 | 8 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0009419 | 0.0002080 | 630.1012 | -4.5272532 | 0.0000699 | 8 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0033096 | 0.0002249 | 630.1012 | -14.7139826 | 0.0000000 | 8 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0031564 | 0.0002531 | 630.1012 | -12.4733969 | 0.0000000 | 8 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0005096 | 0.0002243 | 630.1012 | 2.2720546 | 0.1553620 | 8 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0018581 | 0.0002400 | 630.1012 | -7.7410453 | 0.0000000 | 8 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0036660 | 0.0002650 | 630.1012 | 13.8344658 | 0.0000000 | 8 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0012983 | 0.0002784 | 630.1012 | 4.6627614 | 0.0000374 | 8 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0023677 | 0.0002526 | 630.1012 | -9.3737543 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0020009 | 0.0001926 | 630.1012 | -10.3885469 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0052729 | 0.0002388 | 630.1012 | -22.0836020 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0015167 | 0.0002080 | 630.1012 | -7.2904244 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0037314 | 0.0002249 | 630.1012 | -16.5895812 | 0.0000000 | 8 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0032721 | 0.0002531 | 630.1012 | -12.9303112 | 0.0000000 | 8 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0004842 | 0.0002243 | 630.1012 | 2.1586537 | 0.1969751 | 8 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0017306 | 0.0002400 | 630.1012 | -7.2096669 | 0.0000000 | 8 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0037562 | 0.0002650 | 630.1012 | 14.1748115 | 0.0000000 | 8 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0015415 | 0.0002784 | 630.1012 | 5.5360841 | 0.0000005 | 8 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0022147 | 0.0002526 | 630.1012 | -8.7680936 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0016379 | 0.0001926 | 630.1012 | -8.5037740 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0046015 | 0.0002388 | 630.1012 | -19.2714578 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0008229 | 0.0002080 | 630.1012 | -3.9554378 | 0.0008075 | 8 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0034985 | 0.0002249 | 630.1012 | -15.5540680 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0029636 | 0.0002531 | 630.1012 | -11.7114181 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0008150 | 0.0002243 | 630.1012 | 3.6335453 | 0.0027878 | 8 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0018607 | 0.0002400 | 630.1012 | -7.7516758 | 0.0000000 | 8 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0037786 | 0.0002650 | 630.1012 | 14.2591805 | 0.0000000 | 8 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0011029 | 0.0002784 | 630.1012 | 3.9611044 | 0.0007894 | 8 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0026756 | 0.0002526 | 630.1012 | -10.5928058 | 0.0000000 | 8 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0009670 | 0.0002020 | 622.7189 | -4.7865984 | 0.0000209 | 9 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0046635 | 0.0002504 | 622.7189 | -18.6211034 | 0.0000000 | 9 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0009076 | 0.0002182 | 622.7189 | -4.1592306 | 0.0003503 | 9 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0034326 | 0.0002359 | 622.7189 | -14.5497417 | 0.0000000 | 9 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0036965 | 0.0002654 | 622.7189 | -13.9269870 | 0.0000000 | 9 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000594 | 0.0002353 | 622.7189 | 0.2524599 | 0.9991039 | 9 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0024656 | 0.0002518 | 622.7189 | -9.7932369 | 0.0000000 | 9 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0037559 | 0.0002779 | 622.7189 | 13.5131842 | 0.0000000 | 9 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0012309 | 0.0002921 | 622.7189 | 4.2147044 | 0.0002770 | 9 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0025250 | 0.0002649 | 622.7189 | -9.5306177 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0014238 | 0.0002020 | 622.7189 | -7.0478436 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0054288 | 0.0002504 | 622.7189 | -21.6771002 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0014196 | 0.0002182 | 622.7189 | -6.5055944 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0037863 | 0.0002359 | 622.7189 | -16.0492072 | 0.0000000 | 9 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0040050 | 0.0002654 | 622.7189 | -15.0894294 | 0.0000000 | 9 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000042 | 0.0002353 | 622.7189 | 0.0178652 | 1.0000000 | 9 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0023625 | 0.0002518 | 622.7189 | -9.3838974 | 0.0000000 | 9 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0040092 | 0.0002779 | 622.7189 | 14.4246920 | 0.0000000 | 9 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0016425 | 0.0002921 | 622.7189 | 5.6240134 | 0.0000003 | 9 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0023667 | 0.0002649 | 622.7189 | -8.9333145 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0011353 | 0.0002020 | 622.7189 | -5.6198815 | 0.0000003 | 9 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0048050 | 0.0002504 | 622.7189 | -19.1862858 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0007718 | 0.0002182 | 622.7189 | -3.5367896 | 0.0039676 | 9 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0036449 | 0.0002359 | 622.7189 | -15.4496997 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0036697 | 0.0002654 | 622.7189 | -13.8260429 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0003636 | 0.0002353 | 622.7189 | 1.5453785 | 0.5332710 | 9 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0025096 | 0.0002518 | 622.7189 | -9.9679242 | 0.0000000 | 9 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0040333 | 0.0002779 | 622.7189 | 14.5111111 | 0.0000000 | 9 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0011601 | 0.0002921 | 622.7189 | 3.9723762 | 0.0007553 | 9 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0028731 | 0.0002649 | 622.7189 | -10.8446819 | 0.0000000 | 9 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0010874 | 0.0001749 | 626.1417 | -6.2164281 | 0.0000000 | 10 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0039478 | 0.0002168 | 626.1417 | -18.2054827 | 0.0000000 | 10 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0006912 | 0.0001889 | 626.1417 | -3.6581915 | 0.0025459 | 10 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0031931 | 0.0002043 | 626.1417 | -15.6313950 | 0.0000000 | 10 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0028604 | 0.0002298 | 626.1417 | -12.4465504 | 0.0000000 | 10 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003962 | 0.0002037 | 626.1417 | 1.9450439 | 0.2946378 | 10 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0021057 | 0.0002180 | 626.1417 | -9.6595124 | 0.0000000 | 10 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0032566 | 0.0002407 | 626.1417 | 13.5320479 | 0.0000000 | 10 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0007547 | 0.0002529 | 626.1417 | 2.9845479 | 0.0245333 | 10 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0025019 | 0.0002294 | 626.1417 | -10.9064875 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0015247 | 0.0001749 | 626.1417 | -8.7164454 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0046306 | 0.0002168 | 626.1417 | -21.3542536 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0011621 | 0.0001889 | 626.1417 | -6.1505598 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0036710 | 0.0002043 | 626.1417 | -17.9710118 | 0.0000000 | 10 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0031059 | 0.0002298 | 626.1417 | -13.5147965 | 0.0000000 | 10 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003626 | 0.0002037 | 626.1417 | 1.7800623 | 0.3861436 | 10 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0021463 | 0.0002180 | 626.1417 | -9.8458560 | 0.0000000 | 10 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0034685 | 0.0002407 | 626.1417 | 14.4125238 | 0.0000000 | 10 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0009596 | 0.0002529 | 626.1417 | 3.7947418 | 0.0015191 | 10 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0025089 | 0.0002294 | 626.1417 | -10.9370712 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0012013 | 0.0001749 | 626.1417 | -6.8678015 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0041689 | 0.0002168 | 626.1417 | -19.2250673 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0005814 | 0.0001889 | 626.1417 | -3.0773001 | 0.0184835 | 10 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0034282 | 0.0002043 | 626.1417 | -16.7823108 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0029676 | 0.0002298 | 626.1417 | -12.9128181 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0006199 | 0.0002037 | 626.1417 | 3.0432112 | 0.0205333 | 10 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0022269 | 0.0002180 | 626.1417 | -10.2153282 | 0.0000000 | 10 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0035875 | 0.0002407 | 626.1417 | 14.9067938 | 0.0000000 | 10 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0007407 | 0.0002529 | 626.1417 | 2.9291549 | 0.0289217 | 10 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0028467 | 0.0002294 | 626.1417 | -12.4098040 | 0.0000000 | 10 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0014214 | 0.0001955 | 623.5183 | -7.2691170 | 0.0000000 | 11 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0043086 | 0.0002424 | 623.5183 | -17.7742435 | 0.0000000 | 11 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0008648 | 0.0002112 | 623.5183 | -4.0946807 | 0.0004584 | 11 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0036206 | 0.0002284 | 623.5183 | -15.8554625 | 0.0000000 | 11 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0028872 | 0.0002569 | 623.5183 | -11.2384264 | 0.0000000 | 11 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0005565 | 0.0002277 | 623.5183 | 2.4441503 | 0.1051370 | 11 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0021992 | 0.0002437 | 623.5183 | -9.0247957 | 0.0000000 | 11 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0034438 | 0.0002690 | 623.5183 | 12.8007987 | 0.0000000 | 11 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0006880 | 0.0002827 | 623.5183 | 2.4337520 | 0.1077584 | 11 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0027558 | 0.0002564 | 623.5183 | -10.7465072 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0018680 | 0.0001955 | 623.5183 | -9.5529109 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0049399 | 0.0002424 | 623.5183 | -20.3782727 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0014279 | 0.0002112 | 623.5183 | -6.7606011 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0040539 | 0.0002284 | 623.5183 | -17.7526824 | 0.0000000 | 11 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0030719 | 0.0002569 | 623.5183 | -11.9572470 | 0.0000000 | 11 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0004400 | 0.0002277 | 623.5183 | 1.9325106 | 0.3011351 | 11 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0021859 | 0.0002437 | 623.5183 | -8.9700839 | 0.0000000 | 11 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0035119 | 0.0002690 | 623.5183 | 13.0541821 | 0.0000000 | 11 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0008860 | 0.0002827 | 623.5183 | 3.1341868 | 0.0154671 | 11 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0026260 | 0.0002564 | 623.5183 | -10.2401994 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0015101 | 0.0001955 | 623.5183 | -7.7227364 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0044835 | 0.0002424 | 623.5183 | -18.4954733 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0007548 | 0.0002112 | 623.5183 | -3.5735260 | 0.0034748 | 11 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0037782 | 0.0002284 | 623.5183 | -16.5455945 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0029734 | 0.0002569 | 623.5183 | -11.5736924 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0007553 | 0.0002277 | 623.5183 | 3.3170905 | 0.0085143 | 11 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0022681 | 0.0002437 | 623.5183 | -9.3075066 | 0.0000000 | 11 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0037287 | 0.0002690 | 623.5183 | 13.8598135 | 0.0000000 | 11 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0007052 | 0.0002827 | 623.5183 | 2.4947337 | 0.0930927 | 11 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0030235 | 0.0002564 | 623.5183 | -11.7903015 | 0.0000000 | 11 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0012389 | 0.0002167 | 630.4754 | -5.7179370 | 0.0000002 | 12 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0043150 | 0.0002686 | 630.4754 | -16.0637948 | 0.0000000 | 12 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0008773 | 0.0002340 | 630.4754 | -3.7484051 | 0.0018128 | 12 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0037226 | 0.0002530 | 630.4754 | -14.7116726 | 0.0000000 | 12 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0030760 | 0.0002847 | 630.4754 | -10.8051470 | 0.0000000 | 12 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003617 | 0.0002523 | 630.4754 | 1.4332954 | 0.6063265 | 12 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0024837 | 0.0002700 | 630.4754 | -9.1976661 | 0.0000000 | 12 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0034377 | 0.0002981 | 630.4754 | 11.5314557 | 0.0000000 | 12 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005923 | 0.0003132 | 630.4754 | 1.8909609 | 0.3232130 | 12 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0028453 | 0.0002842 | 630.4754 | -10.0131858 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0017589 | 0.0002167 | 630.4754 | -8.1177207 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0050468 | 0.0002686 | 630.4754 | -18.7882745 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0014243 | 0.0002340 | 630.4754 | -6.0857113 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0039907 | 0.0002530 | 630.4754 | -15.7709406 | 0.0000000 | 12 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0032879 | 0.0002847 | 630.4754 | -11.5493379 | 0.0000000 | 12 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003346 | 0.0002523 | 630.4754 | 1.3260696 | 0.6750394 | 12 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0022318 | 0.0002700 | 630.4754 | -8.2646700 | 0.0000000 | 12 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0036225 | 0.0002981 | 630.4754 | 12.1513612 | 0.0000000 | 12 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0010561 | 0.0003132 | 630.4754 | 3.3715777 | 0.0070742 | 12 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0025664 | 0.0002842 | 630.4754 | -9.0313541 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0014038 | 0.0002167 | 630.4754 | -6.4789055 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0045536 | 0.0002686 | 630.4754 | -16.9521030 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0008387 | 0.0002340 | 630.4754 | -3.5832924 | 0.0033511 | 12 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0040962 | 0.0002530 | 630.4754 | -16.1878915 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0031498 | 0.0002847 | 630.4754 | -11.0641321 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0005652 | 0.0002523 | 630.4754 | 2.2399150 | 0.1664425 | 12 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0026924 | 0.0002700 | 630.4754 | -9.9703718 | 0.0000000 | 12 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0037149 | 0.0002981 | 630.4754 | 12.4614929 | 0.0000000 | 12 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004574 | 0.0003132 | 630.4754 | 1.4602176 | 0.5888040 | 12 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0032575 | 0.0002842 | 630.4754 | -11.4637287 | 0.0000000 | 12 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0010116 | 0.0001894 | 639.1797 | -5.3420672 | 0.0000013 | 13 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0041622 | 0.0002348 | 639.1797 | -17.7301525 | 0.0000000 | 13 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0008443 | 0.0002045 | 639.1797 | -4.1278110 | 0.0003983 | 13 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0031188 | 0.0002211 | 639.1797 | -14.1030464 | 0.0000000 | 13 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0031506 | 0.0002488 | 639.1797 | -12.6635410 | 0.0000000 | 13 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001673 | 0.0002205 | 639.1797 | 0.7586019 | 0.9422196 | 13 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0021072 | 0.0002360 | 639.1797 | -8.9289446 | 0.0000000 | 13 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0033179 | 0.0002605 | 639.1797 | 12.7350603 | 0.0000000 | 13 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0010434 | 0.0002738 | 639.1797 | 3.8115371 | 0.0014213 | 13 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0022745 | 0.0002483 | 639.1797 | -9.1587208 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0014869 | 0.0001894 | 639.1797 | -7.8521398 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0049285 | 0.0002348 | 639.1797 | -20.9943993 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0013932 | 0.0002045 | 639.1797 | -6.8115103 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0038451 | 0.0002211 | 639.1797 | -17.3873847 | 0.0000000 | 13 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0034416 | 0.0002488 | 639.1797 | -13.8330924 | 0.0000000 | 13 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000937 | 0.0002205 | 639.1797 | 0.4247838 | 0.9931976 | 13 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0023582 | 0.0002360 | 639.1797 | -9.9924832 | 0.0000000 | 13 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0035353 | 0.0002605 | 639.1797 | 13.5693745 | 0.0000000 | 13 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0010834 | 0.0002738 | 639.1797 | 3.9576118 | 0.0007994 | 13 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0024518 | 0.0002483 | 639.1797 | -9.8729767 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0011737 | 0.0001894 | 639.1797 | -6.1981607 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0042709 | 0.0002348 | 639.1797 | -18.1933113 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0007486 | 0.0002045 | 639.1797 | -3.6598952 | 0.0025260 | 13 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0034515 | 0.0002211 | 639.1797 | -15.6076484 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0030972 | 0.0002488 | 639.1797 | -12.4489696 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004251 | 0.0002205 | 639.1797 | 1.9277768 | 0.3035797 | 13 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0022778 | 0.0002360 | 639.1797 | -9.6519183 | 0.0000000 | 13 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0035223 | 0.0002605 | 639.1797 | 13.5197433 | 0.0000000 | 13 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0008194 | 0.0002738 | 639.1797 | 2.9932930 | 0.0238810 | 13 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0027029 | 0.0002483 | 639.1797 | -10.8839383 | 0.0000000 | 13 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0014573 | 0.0002031 | 629.1835 | -7.1750953 | 0.0000000 | 14 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0041591 | 0.0002518 | 629.1835 | -16.5181164 | 0.0000000 | 14 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0007848 | 0.0002194 | 629.1835 | -3.5770367 | 0.0034287 | 14 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0034408 | 0.0002372 | 629.1835 | -14.5066154 | 0.0000000 | 14 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0027018 | 0.0002669 | 629.1835 | -10.1247544 | 0.0000000 | 14 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0006726 | 0.0002365 | 629.1835 | 2.8435576 | 0.0370395 | 14 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0019835 | 0.0002531 | 629.1835 | -7.8362844 | 0.0000000 | 14 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0033744 | 0.0002794 | 629.1835 | 12.0753608 | 0.0000000 | 14 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0007183 | 0.0002936 | 629.1835 | 2.4461938 | 0.1046155 | 14 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0026561 | 0.0002664 | 629.1835 | -9.9717311 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0019261 | 0.0002031 | 629.1835 | -9.4832583 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0050255 | 0.0002518 | 629.1835 | -19.9590968 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0013647 | 0.0002194 | 629.1835 | -6.2207193 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0038465 | 0.0002372 | 629.1835 | -16.2166672 | 0.0000000 | 14 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0030994 | 0.0002669 | 629.1835 | -11.6147426 | 0.0000000 | 14 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0005614 | 0.0002365 | 629.1835 | 2.3734712 | 0.1239617 | 14 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0019203 | 0.0002531 | 629.1835 | -7.5866305 | 0.0000000 | 14 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0036608 | 0.0002794 | 629.1835 | 13.1003372 | 0.0000000 | 14 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0011791 | 0.0002936 | 629.1835 | 4.0155222 | 0.0006337 | 14 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0024817 | 0.0002664 | 629.1835 | -9.3170689 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0016062 | 0.0002031 | 629.1835 | -7.9083633 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0044053 | 0.0002518 | 629.1835 | -17.4959964 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0007646 | 0.0002194 | 629.1835 | -3.4850092 | 0.0047685 | 14 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0036953 | 0.0002372 | 629.1835 | -15.5792335 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0027991 | 0.0002669 | 629.1835 | -10.4893395 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0008417 | 0.0002365 | 629.1835 | 3.5585990 | 0.0036655 | 14 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0020890 | 0.0002531 | 629.1835 | -8.2530176 | 0.0000000 | 14 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0036408 | 0.0002794 | 629.1835 | 13.0287286 | 0.0000000 | 14 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0007101 | 0.0002936 | 629.1835 | 2.4182868 | 0.1117392 | 14 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0029307 | 0.0002664 | 629.1835 | -11.0026781 | 0.0000000 | 14 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0010614 | 0.0002245 | 625.9843 | -4.7276363 | 0.0000276 | 15 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0047660 | 0.0002783 | 625.9843 | -17.1244395 | 0.0000000 | 15 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0011094 | 0.0002425 | 625.9843 | -4.5747598 | 0.0000563 | 15 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0036459 | 0.0002622 | 625.9843 | -13.9065239 | 0.0000000 | 15 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0037046 | 0.0002950 | 625.9843 | -12.5596691 | 0.0000000 | 15 |
| Beagle | SUPER | AMR - EUR | 0 | -0.0000480 | 0.0002614 | 625.9843 | -0.1836016 | 0.9997458 | 15 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0025846 | 0.0002798 | 625.9843 | -9.2378127 | 0.0000000 | 15 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0036566 | 0.0003089 | 625.9843 | 11.8383898 | 0.0000000 | 15 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0011200 | 0.0003246 | 625.9843 | 3.4508776 | 0.0053787 | 15 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0025366 | 0.0002944 | 625.9843 | -8.6155968 | 0.0000000 | 15 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0014429 | 0.0002245 | 625.9843 | -6.4272183 | 0.0000000 | 15 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0053909 | 0.0002783 | 625.9843 | -19.3698530 | 0.0000000 | 15 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0015275 | 0.0002425 | 625.9843 | -6.2991073 | 0.0000000 | 15 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0041471 | 0.0002622 | 625.9843 | -15.8180651 | 0.0000000 | 15 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0039480 | 0.0002950 | 625.9843 | -13.3847692 | 0.0000000 | 15 |
| Eagle | SUPER | AMR - EUR | 0 | -0.0000846 | 0.0002614 | 625.9843 | -0.3235557 | 0.9976281 | 15 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0027042 | 0.0002798 | 625.9843 | -9.6652951 | 0.0000000 | 15 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0038634 | 0.0003089 | 625.9843 | 12.5078580 | 0.0000000 | 15 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0012438 | 0.0003246 | 625.9843 | 3.8322244 | 0.0013141 | 15 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0026196 | 0.0002944 | 625.9843 | -8.8975567 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0012750 | 0.0002245 | 625.9843 | -5.6793027 | 0.0000002 | 15 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0050149 | 0.0002783 | 625.9843 | -18.0189972 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0010286 | 0.0002425 | 625.9843 | -4.2419313 | 0.0002465 | 15 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0040806 | 0.0002622 | 625.9843 | -15.5645729 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0037399 | 0.0002950 | 625.9843 | -12.6794070 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0002464 | 0.0002614 | 625.9843 | 0.9423430 | 0.8802320 | 15 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0028056 | 0.0002798 | 625.9843 | -10.0278877 | 0.0000000 | 15 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0039863 | 0.0003089 | 625.9843 | 12.9057295 | 0.0000000 | 15 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0009343 | 0.0003246 | 625.9843 | 2.8786119 | 0.0335069 | 15 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0030520 | 0.0002944 | 625.9843 | -10.3661934 | 0.0000000 | 15 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0014752 | 0.0002468 | 635.1038 | -5.9760746 | 0.0000000 | 16 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0052671 | 0.0003060 | 635.1038 | -17.2117779 | 0.0000000 | 16 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0008846 | 0.0002666 | 635.1038 | -3.3177969 | 0.0084863 | 16 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0040924 | 0.0002883 | 635.1038 | -14.1961532 | 0.0000000 | 16 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0037919 | 0.0003243 | 635.1038 | -11.6918664 | 0.0000000 | 16 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0005905 | 0.0002875 | 635.1038 | 2.0543818 | 0.2415070 | 16 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0026172 | 0.0003076 | 635.1038 | -8.5074612 | 0.0000000 | 16 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0043825 | 0.0003396 | 635.1038 | 12.9039097 | 0.0000000 | 16 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0011747 | 0.0003569 | 635.1038 | 3.2918106 | 0.0092581 | 16 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0032078 | 0.0003237 | 635.1038 | -9.9087891 | 0.0000000 | 16 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0017876 | 0.0002468 | 635.1038 | -7.2415754 | 0.0000000 | 16 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0058365 | 0.0003060 | 635.1038 | -19.0723537 | 0.0000000 | 16 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0015439 | 0.0002666 | 635.1038 | -5.7903934 | 0.0000001 | 16 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0040591 | 0.0002883 | 635.1038 | -14.0806415 | 0.0000000 | 16 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0040489 | 0.0003243 | 635.1038 | -12.4842363 | 0.0000000 | 16 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002437 | 0.0002875 | 635.1038 | 0.8476218 | 0.9155117 | 16 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0022715 | 0.0003076 | 635.1038 | -7.3837761 | 0.0000000 | 16 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0042926 | 0.0003396 | 635.1038 | 12.6391805 | 0.0000000 | 16 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0017774 | 0.0003569 | 635.1038 | 4.9805965 | 0.0000081 | 16 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0025152 | 0.0003237 | 635.1038 | -7.7694042 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0017040 | 0.0002468 | 635.1038 | -6.9028705 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0054842 | 0.0003060 | 635.1038 | -17.9211335 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0010933 | 0.0002666 | 635.1038 | -4.1003796 | 0.0004468 | 16 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0042918 | 0.0002883 | 635.1038 | -14.8879181 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0037802 | 0.0003243 | 635.1038 | -11.6557840 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0006107 | 0.0002875 | 635.1038 | 2.1243569 | 0.2109475 | 16 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0025878 | 0.0003076 | 635.1038 | -8.4120234 | 0.0000000 | 16 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0043909 | 0.0003396 | 635.1038 | 12.9286797 | 0.0000000 | 16 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0011924 | 0.0003569 | 635.1038 | 3.3412908 | 0.0078393 | 16 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0031985 | 0.0003237 | 635.1038 | -9.8802303 | 0.0000000 | 16 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0014479 | 0.0002472 | 628.8503 | -5.8566941 | 0.0000001 | 17 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0056484 | 0.0003065 | 628.8503 | -18.4294160 | 0.0000000 | 17 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0011418 | 0.0002670 | 628.8503 | -4.2757689 | 0.0002130 | 17 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0041924 | 0.0002887 | 628.8503 | -14.5208586 | 0.0000000 | 17 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0042004 | 0.0003248 | 628.8503 | -12.9316463 | 0.0000000 | 17 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003061 | 0.0002879 | 628.8503 | 1.0632881 | 0.8252635 | 17 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0027445 | 0.0003081 | 628.8503 | -8.9075221 | 0.0000000 | 17 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0045066 | 0.0003401 | 628.8503 | 13.2489718 | 0.0000000 | 17 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0014560 | 0.0003574 | 628.8503 | 4.0736608 | 0.0004995 | 17 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0030506 | 0.0003242 | 628.8503 | -9.4089123 | 0.0000000 | 17 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0017465 | 0.0002472 | 628.8503 | -7.0645036 | 0.0000000 | 17 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0061128 | 0.0003065 | 628.8503 | -19.9446338 | 0.0000000 | 17 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0015395 | 0.0002670 | 628.8503 | -5.7651733 | 0.0000001 | 17 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0045982 | 0.0002887 | 628.8503 | -15.9262824 | 0.0000000 | 17 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0043662 | 0.0003248 | 628.8503 | -13.4420597 | 0.0000000 | 17 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002070 | 0.0002879 | 628.8503 | 0.7189578 | 0.9521363 | 17 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0028516 | 0.0003081 | 628.8503 | -9.2553411 | 0.0000000 | 17 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0045732 | 0.0003401 | 628.8503 | 13.4449481 | 0.0000000 | 17 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0015146 | 0.0003574 | 628.8503 | 4.2376915 | 0.0002508 | 17 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0030586 | 0.0003242 | 628.8503 | -9.4336907 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0014701 | 0.0002472 | 628.8503 | -5.9463243 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0056849 | 0.0003065 | 628.8503 | -18.5484581 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0009867 | 0.0002670 | 628.8503 | -3.6947700 | 0.0022204 | 17 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0043024 | 0.0002887 | 628.8503 | -14.9019417 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0042148 | 0.0003248 | 628.8503 | -12.9757506 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004834 | 0.0002879 | 628.8503 | 1.6791685 | 0.4476166 | 17 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0028323 | 0.0003081 | 628.8503 | -9.1927013 | 0.0000000 | 17 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0046982 | 0.0003401 | 628.8503 | 13.8123685 | 0.0000000 | 17 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0013824 | 0.0003574 | 628.8503 | 3.8679043 | 0.0011428 | 17 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0033158 | 0.0003242 | 628.8503 | -10.2267934 | 0.0000000 | 17 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0015084 | 0.0001993 | 629.0274 | -7.5676517 | 0.0000000 | 18 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0047960 | 0.0002471 | 629.0274 | -19.4097899 | 0.0000000 | 18 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0011030 | 0.0002153 | 629.0274 | -5.1233338 | 0.0000040 | 18 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0036308 | 0.0002328 | 629.0274 | -15.5986571 | 0.0000000 | 18 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0032877 | 0.0002619 | 629.0274 | -12.5544450 | 0.0000000 | 18 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0004053 | 0.0002321 | 629.0274 | 1.7463725 | 0.4062741 | 18 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0021225 | 0.0002484 | 629.0274 | -8.5446072 | 0.0000000 | 18 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0036930 | 0.0002742 | 629.0274 | 13.4669262 | 0.0000000 | 18 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0011652 | 0.0002881 | 629.0274 | 4.0437078 | 0.0005649 | 18 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0025278 | 0.0002614 | 629.0274 | -9.6705886 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0018831 | 0.0001993 | 629.0274 | -9.4479626 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0054796 | 0.0002471 | 629.0274 | -22.1761324 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0016680 | 0.0002153 | 629.0274 | -7.7474975 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0039868 | 0.0002328 | 629.0274 | -17.1281809 | 0.0000000 | 18 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0035964 | 0.0002619 | 629.0274 | -13.7335174 | 0.0000000 | 18 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002152 | 0.0002321 | 629.0274 | 0.9269811 | 0.8864313 | 18 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0021037 | 0.0002484 | 629.0274 | -8.4690977 | 0.0000000 | 18 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0038116 | 0.0002742 | 629.0274 | 13.8993445 | 0.0000000 | 18 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0014927 | 0.0002881 | 629.0274 | 5.1803522 | 0.0000030 | 18 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0023189 | 0.0002614 | 629.0274 | -8.8712456 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0016083 | 0.0001993 | 629.0274 | -8.0689797 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0048672 | 0.0002471 | 629.0274 | -19.6978321 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0009872 | 0.0002153 | 629.0274 | -4.5852150 | 0.0000536 | 18 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0037775 | 0.0002328 | 629.0274 | -16.2286496 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0032589 | 0.0002619 | 629.0274 | -12.4446596 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0006211 | 0.0002321 | 629.0274 | 2.6760167 | 0.0586925 | 18 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0021692 | 0.0002484 | 629.0274 | -8.7326821 | 0.0000000 | 18 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0038800 | 0.0002742 | 629.0274 | 14.1489358 | 0.0000000 | 18 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0010897 | 0.0002881 | 629.0274 | 3.7818038 | 0.0015960 | 18 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0027903 | 0.0002614 | 629.0274 | -10.6748020 | 0.0000000 | 18 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0013213 | 0.0002242 | 634.4979 | -5.8929134 | 0.0000001 | 19 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0050518 | 0.0002780 | 634.4979 | -18.1740966 | 0.0000000 | 19 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0009680 | 0.0002422 | 634.4979 | -3.9968421 | 0.0006830 | 19 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0035872 | 0.0002618 | 634.4979 | -13.6997028 | 0.0000000 | 19 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0037304 | 0.0002946 | 634.4979 | -12.6631694 | 0.0000000 | 19 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003533 | 0.0002611 | 634.4979 | 1.3531124 | 0.6579387 | 19 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0022659 | 0.0002794 | 634.4979 | -8.1089849 | 0.0000000 | 19 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0040838 | 0.0003085 | 634.4979 | 13.2378978 | 0.0000000 | 19 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0014645 | 0.0003242 | 634.4979 | 4.5180460 | 0.0000728 | 19 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0026192 | 0.0002941 | 634.4979 | -8.9074205 | 0.0000000 | 19 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0017241 | 0.0002242 | 634.4979 | -7.6891767 | 0.0000000 | 19 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0055256 | 0.0002780 | 634.4979 | -19.8788073 | 0.0000000 | 19 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0013803 | 0.0002422 | 634.4979 | -5.6990356 | 0.0000002 | 19 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0038162 | 0.0002618 | 634.4979 | -14.5740844 | 0.0000000 | 19 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0038015 | 0.0002946 | 634.4979 | -12.9044968 | 0.0000000 | 19 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003438 | 0.0002611 | 634.4979 | 1.3167309 | 0.6808961 | 19 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0020921 | 0.0002794 | 634.4979 | -7.4870059 | 0.0000000 | 19 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0041453 | 0.0003085 | 634.4979 | 13.4375588 | 0.0000000 | 19 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0017094 | 0.0003242 | 634.4979 | 5.2735435 | 0.0000018 | 19 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0024359 | 0.0002941 | 634.4979 | -8.2840530 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0014333 | 0.0002242 | 634.4979 | -6.3923738 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0052570 | 0.0002780 | 634.4979 | -18.9124522 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0009033 | 0.0002422 | 634.4979 | -3.7298200 | 0.0019443 | 19 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0038854 | 0.0002618 | 634.4979 | -14.8386242 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0038237 | 0.0002946 | 634.4979 | -12.9797041 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0005300 | 0.0002611 | 634.4979 | 2.0296942 | 0.2529362 | 19 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0024522 | 0.0002794 | 634.4979 | -8.7754567 | 0.0000000 | 19 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0043537 | 0.0003085 | 634.4979 | 14.1128280 | 0.0000000 | 19 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0013715 | 0.0003242 | 634.4979 | 4.2311831 | 0.0002576 | 19 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0029821 | 0.0002941 | 634.4979 | -10.1415417 | 0.0000000 | 19 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0017747 | 0.0002477 | 624.9958 | -7.1648970 | 0.0000000 | 20 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0057185 | 0.0003071 | 624.9958 | -18.6226969 | 0.0000000 | 20 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0010484 | 0.0002676 | 624.9958 | -3.9184499 | 0.0009367 | 20 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0040930 | 0.0002893 | 624.9958 | -14.1496900 | 0.0000000 | 20 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0039438 | 0.0003254 | 624.9958 | -12.1183187 | 0.0000000 | 20 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0007263 | 0.0002884 | 624.9958 | 2.5181183 | 0.0879064 | 20 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0023183 | 0.0003087 | 624.9958 | -7.5100060 | 0.0000000 | 20 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0046701 | 0.0003408 | 624.9958 | 13.7036535 | 0.0000000 | 20 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0016255 | 0.0003581 | 624.9958 | 4.5392309 | 0.0000663 | 20 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0030446 | 0.0003248 | 624.9958 | -9.3726940 | 0.0000000 | 20 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0021922 | 0.0002477 | 624.9958 | -8.8501815 | 0.0000000 | 20 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0063671 | 0.0003071 | 624.9958 | -20.7348940 | 0.0000000 | 20 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0015824 | 0.0002676 | 624.9958 | -5.9145031 | 0.0000001 | 20 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0044268 | 0.0002893 | 624.9958 | -15.3035387 | 0.0000000 | 20 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0041749 | 0.0003254 | 624.9958 | -12.8286031 | 0.0000000 | 20 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0006097 | 0.0002884 | 624.9958 | 2.1138627 | 0.2153785 | 20 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0022346 | 0.0003087 | 624.9958 | -7.2389551 | 0.0000000 | 20 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0047846 | 0.0003408 | 624.9958 | 14.0397749 | 0.0000000 | 20 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0019403 | 0.0003581 | 624.9958 | 5.4184029 | 0.0000009 | 20 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0028444 | 0.0003248 | 624.9958 | -8.7561534 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0019839 | 0.0002477 | 624.9958 | -8.0095161 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0059898 | 0.0003071 | 624.9958 | -19.5063328 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0010475 | 0.0002676 | 624.9958 | -3.9152178 | 0.0009488 | 20 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0043254 | 0.0002893 | 624.9958 | -14.9529285 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0040059 | 0.0003254 | 624.9958 | -12.3092271 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0009364 | 0.0002884 | 624.9958 | 3.2464170 | 0.0107676 | 20 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0023414 | 0.0003087 | 624.9958 | -7.5849650 | 0.0000000 | 20 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0049423 | 0.0003408 | 624.9958 | 14.5023907 | 0.0000000 | 20 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0016645 | 0.0003581 | 624.9958 | 4.6481116 | 0.0000401 | 20 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0032778 | 0.0003248 | 624.9958 | -10.0906273 | 0.0000000 | 20 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0007372 | 0.0002263 | 643.1741 | -3.2576924 | 0.0103616 | 21 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0036969 | 0.0002806 | 643.1741 | -13.1770282 | 0.0000000 | 21 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003914 | 0.0002444 | 643.1741 | -1.6011994 | 0.4971217 | 21 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0028476 | 0.0002643 | 643.1741 | -10.7746926 | 0.0000000 | 21 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0029596 | 0.0002973 | 643.1741 | -9.9538464 | 0.0000000 | 21 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003458 | 0.0002635 | 643.1741 | 1.3122716 | 0.6836824 | 21 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0021104 | 0.0002820 | 643.1741 | -7.4825790 | 0.0000000 | 21 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0033054 | 0.0003114 | 643.1741 | 10.6160764 | 0.0000000 | 21 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0008493 | 0.0003272 | 643.1741 | 2.5957829 | 0.0723010 | 21 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0024562 | 0.0002968 | 643.1741 | -8.2758864 | 0.0000000 | 21 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0011533 | 0.0002263 | 643.1741 | -5.0959624 | 0.0000045 | 21 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0042066 | 0.0002806 | 643.1741 | -14.9940614 | 0.0000000 | 21 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0008309 | 0.0002444 | 643.1741 | -3.3992532 | 0.0064259 | 21 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0032272 | 0.0002643 | 643.1741 | -12.2111418 | 0.0000000 | 21 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0030534 | 0.0002973 | 643.1741 | -10.2691848 | 0.0000000 | 21 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003223 | 0.0002635 | 643.1741 | 1.2230462 | 0.7379489 | 21 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0020740 | 0.0002820 | 643.1741 | -7.3535865 | 0.0000000 | 21 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0033757 | 0.0003114 | 643.1741 | 10.8416870 | 0.0000000 | 21 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0009794 | 0.0003272 | 643.1741 | 2.9935632 | 0.0238569 | 21 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0023963 | 0.0002968 | 643.1741 | -8.0740772 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0008927 | 0.0002263 | 643.1741 | -3.9446457 | 0.0008415 | 21 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0037265 | 0.0002806 | 643.1741 | -13.2827307 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003472 | 0.0002444 | 643.1741 | -1.4202424 | 0.6147922 | 21 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0030795 | 0.0002643 | 643.1741 | -11.6520154 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0028338 | 0.0002973 | 643.1741 | -9.5307290 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0005455 | 0.0002635 | 643.1741 | 2.0700286 | 0.2344216 | 21 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0021868 | 0.0002820 | 643.1741 | -7.7534713 | 0.0000000 | 21 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0033793 | 0.0003114 | 643.1741 | 10.8533863 | 0.0000000 | 21 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0006471 | 0.0003272 | 643.1741 | 1.9777273 | 0.2780590 | 21 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0027323 | 0.0002968 | 643.1741 | -9.2061716 | 0.0000000 | 21 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0010292 | 0.0002758 | 635.3619 | -3.7317389 | 0.0019300 | 22 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0049191 | 0.0003419 | 635.3619 | -14.3868553 | 0.0000000 | 22 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0006473 | 0.0002979 | 635.3619 | -2.1726565 | 0.1914428 | 22 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0036761 | 0.0003221 | 635.3619 | -11.4131038 | 0.0000000 | 22 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0038899 | 0.0003624 | 635.3619 | -10.7345867 | 0.0000000 | 22 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003820 | 0.0003212 | 635.3619 | 1.1892886 | 0.7575832 | 22 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0026468 | 0.0003437 | 635.3619 | -7.7004335 | 0.0000000 | 22 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0042718 | 0.0003795 | 635.3619 | 11.2575478 | 0.0000000 | 22 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0012430 | 0.0003987 | 635.3619 | 3.1175250 | 0.0162906 | 22 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0030288 | 0.0003617 | 635.3619 | -8.3737080 | 0.0000000 | 22 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0013812 | 0.0002758 | 635.3619 | -5.0079467 | 0.0000071 | 22 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0055010 | 0.0003419 | 635.3619 | -16.0887347 | 0.0000000 | 22 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0010241 | 0.0002979 | 635.3619 | -3.4377523 | 0.0056263 | 22 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0039851 | 0.0003221 | 635.3619 | -12.3727089 | 0.0000000 | 22 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0041198 | 0.0003624 | 635.3619 | -11.3690675 | 0.0000000 | 22 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003571 | 0.0003212 | 635.3619 | 1.1117540 | 0.8003720 | 22 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0026039 | 0.0003437 | 635.3619 | -7.5756091 | 0.0000000 | 22 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0044769 | 0.0003795 | 635.3619 | 11.7978168 | 0.0000000 | 22 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0015159 | 0.0003987 | 635.3619 | 3.8017516 | 0.0014768 | 22 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0029610 | 0.0003617 | 635.3619 | -8.1862407 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0011736 | 0.0002758 | 635.3619 | -4.2550574 | 0.0002325 | 22 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0049986 | 0.0003419 | 635.3619 | -14.6193366 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0006805 | 0.0002979 | 635.3619 | -2.2843712 | 0.1512505 | 22 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0039901 | 0.0003221 | 635.3619 | -12.3882304 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0038250 | 0.0003624 | 635.3619 | -10.5556388 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004930 | 0.0003212 | 635.3619 | 1.5350562 | 0.5399803 | 22 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0028166 | 0.0003437 | 635.3619 | -8.1942754 | 0.0000000 | 22 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0043180 | 0.0003795 | 635.3619 | 11.3793193 | 0.0000000 | 22 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0010085 | 0.0003987 | 635.3619 | 2.5291789 | 0.0855157 | 22 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0033096 | 0.0003617 | 635.3619 | -9.1500304 | 0.0000000 | 22 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0004255 | 0.0000910 | 1048.8670 | -4.6761548 | 0.0000325 | 23 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0028946 | 0.0000910 | 1048.8670 | -31.8102658 | 0.0000000 | 23 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0008571 | 0.0000910 | 1048.8670 | -9.4193721 | 0.0000000 | 23 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0017394 | 0.0000910 | 1048.8670 | -19.1148049 | 0.0000000 | 23 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0024691 | 0.0000910 | 1048.8670 | -27.1341110 | 0.0000000 | 23 |
| Beagle | SUPER | AMR - EUR | 0 | -0.0004316 | 0.0000910 | 1048.8670 | -4.7432172 | 0.0000236 | 23 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0013139 | 0.0000910 | 1048.8670 | -14.4386500 | 0.0000000 | 23 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0020375 | 0.0000910 | 1048.8670 | 22.3908937 | 0.0000000 | 23 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0011552 | 0.0000910 | 1048.8670 | 12.6954609 | 0.0000000 | 23 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008822 | 0.0000910 | 1048.8670 | -9.6954328 | 0.0000000 | 23 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0004013 | 0.0000910 | 1048.8670 | -4.4099380 | 0.0001112 | 23 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0032492 | 0.0000910 | 1048.8670 | -35.7067602 | 0.0000000 | 23 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0009391 | 0.0000910 | 1048.8670 | -10.3203979 | 0.0000000 | 23 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0019586 | 0.0000910 | 1048.8670 | -21.5237585 | 0.0000000 | 23 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0028479 | 0.0000910 | 1048.8670 | -31.2968222 | 0.0000000 | 23 |
| Eagle | SUPER | AMR - EUR | 0 | -0.0005378 | 0.0000910 | 1048.8670 | -5.9104599 | 0.0000000 | 23 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0015573 | 0.0000910 | 1048.8670 | -17.1138205 | 0.0000000 | 23 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0023101 | 0.0000910 | 1048.8670 | 25.3863622 | 0.0000000 | 23 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0012906 | 0.0000910 | 1048.8670 | 14.1830017 | 0.0000000 | 23 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010195 | 0.0000910 | 1048.8670 | -11.2033606 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0004491 | 0.0000910 | 1048.8670 | -4.9351372 | 0.0000092 | 23 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0027998 | 0.0000910 | 1048.8670 | -30.7685457 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0008528 | 0.0000910 | 1048.8670 | -9.3721252 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0016975 | 0.0000910 | 1048.8670 | -18.6541676 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0023507 | 0.0000910 | 1048.8670 | -25.8334085 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AMR - EUR | 0 | -0.0004037 | 0.0000910 | 1048.8670 | -4.4369880 | 0.0000984 | 23 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0012484 | 0.0000910 | 1048.8670 | -13.7190304 | 0.0000000 | 23 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0019470 | 0.0000910 | 1048.8670 | 21.3964205 | 0.0000000 | 23 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0011024 | 0.0000910 | 1048.8670 | 12.1143781 | 0.0000000 | 23 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0008446 | 0.0000910 | 1048.8670 | -9.2820424 | 0.0000000 | 23 |
Next, let’s consider switches and flips independently:
# df_switches <- df_switch_trio[[1]] %>%
# mutate(Eagle = (n_other_eagle) / n_hets,
# Beagle = (n_other_beagle) / n_hets,
# SHAPEIT = (n_other_shapeit) / n_hets) %>%
# select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
# mutate(chrom = 1)
#
# for(i in 2:22){
# df_switches <- bind_rows(df_switches,
# {
# df_switch_trio[[i]] %>%
# mutate(Eagle = (n_other_eagle) / n_hets,
# Beagle = (n_other_beagle) / n_hets,
# SHAPEIT = (n_other_shapeit) / n_hets) %>%
# select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
# mutate(chrom = i)
# })
# }
#
df_switches <- df_switch_trio_noth %>%
mutate(Eagle = (n_switch_e) / n_het,
Beagle = (n_switch_b) / n_het,
SHAPEIT = (n_switch_s) / n_het) %>%
select(Eagle, Beagle, SHAPEIT, sample, chrom)
df_switches <- df_switches %>%
left_join({df_subj_rel %>% select(id2, SUPER)}, by = c("sample" = "id2")) %>%
rename(pair_id = sample) %>%
select(Eagle, Beagle, SHAPEIT, SUPER, pair_id, chrom)
df_switches <- df_switches %>%
bind_rows({df_switch_x %>%
mutate(Eagle = (n_other_eagle) / n_hets,
Beagle = (n_other_beagle) / n_hets,
SHAPEIT = (n_other_shapeit) / n_hets) %>%
rename(SUPER = pop) %>%
select(Eagle, Beagle, SHAPEIT, SUPER) %>%
mutate(pair_id = 603:1602, chrom = 23)})
df_switches %>%
group_by(chrom) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
knitr::kable()
| chrom | Beagle | Eagle | SHAPEIT |
|---|---|---|---|
| 1 | 0.0019084 | 0.0024999 | 0.0018737 |
| 2 | 0.0017862 | 0.0023895 | 0.0017640 |
| 3 | 0.0016596 | 0.0022318 | 0.0016561 |
| 4 | 0.0015058 | 0.0020500 | 0.0014972 |
| 5 | 0.0016545 | 0.0022052 | 0.0016464 |
| 6 | 0.0014645 | 0.0019622 | 0.0014465 |
| 7 | 0.0018935 | 0.0024565 | 0.0018503 |
| 8 | 0.0016766 | 0.0022457 | 0.0016720 |
| 9 | 0.0025877 | 0.0031912 | 0.0025272 |
| 10 | 0.0018561 | 0.0024419 | 0.0018115 |
| 11 | 0.0017216 | 0.0023083 | 0.0016987 |
| 12 | 0.0018425 | 0.0024028 | 0.0018366 |
| 13 | 0.0017893 | 0.0023635 | 0.0017801 |
| 14 | 0.0021114 | 0.0027364 | 0.0021083 |
| 15 | 0.0027363 | 0.0034055 | 0.0027022 |
| 16 | 0.0025976 | 0.0033503 | 0.0025877 |
| 17 | 0.0027715 | 0.0035106 | 0.0027148 |
| 18 | 0.0020664 | 0.0026810 | 0.0020536 |
| 19 | 0.0027082 | 0.0033871 | 0.0026400 |
| 20 | 0.0027694 | 0.0034397 | 0.0026885 |
| 21 | 0.0032355 | 0.0038173 | 0.0032186 |
| 22 | 0.0038186 | 0.0045225 | 0.0036899 |
| 23 | 0.0017000 | 0.0022896 | 0.0015654 |
df_switches %>%
group_by(chrom, SUPER) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
knitr::kable()
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.
| chrom | SUPER | Beagle | Eagle | SHAPEIT |
|---|---|---|---|---|
| 1 | AFR | 0.0013031 | 0.0017879 | 0.0012370 |
| 1 | AMR | 0.0017838 | 0.0023339 | 0.0017660 |
| 1 | EAS | 0.0031973 | 0.0041090 | 0.0032297 |
| 1 | EUR | 0.0017845 | 0.0023154 | 0.0017281 |
| 1 | SAS | 0.0026048 | 0.0033203 | 0.0025879 |
| 2 | AFR | 0.0012032 | 0.0017167 | 0.0011570 |
| 2 | AMR | 0.0017330 | 0.0023111 | 0.0017309 |
| 2 | EAS | 0.0030258 | 0.0038904 | 0.0030452 |
| 2 | EUR | 0.0015921 | 0.0021094 | 0.0015504 |
| 2 | SAS | 0.0024448 | 0.0031883 | 0.0024363 |
| 3 | AFR | 0.0011096 | 0.0016027 | 0.0010764 |
| 3 | AMR | 0.0015866 | 0.0021087 | 0.0015880 |
| 3 | EAS | 0.0027729 | 0.0036531 | 0.0028329 |
| 3 | EUR | 0.0015385 | 0.0020425 | 0.0015186 |
| 3 | SAS | 0.0022871 | 0.0029521 | 0.0023130 |
| 4 | AFR | 0.0009938 | 0.0014277 | 0.0009428 |
| 4 | AMR | 0.0015003 | 0.0020231 | 0.0015086 |
| 4 | EAS | 0.0024240 | 0.0032640 | 0.0025213 |
| 4 | EUR | 0.0013769 | 0.0018891 | 0.0013453 |
| 4 | SAS | 0.0021102 | 0.0027394 | 0.0021138 |
| 5 | AFR | 0.0010981 | 0.0015620 | 0.0010441 |
| 5 | AMR | 0.0015576 | 0.0020605 | 0.0016006 |
| 5 | EAS | 0.0027997 | 0.0036286 | 0.0028362 |
| 5 | EUR | 0.0015035 | 0.0020003 | 0.0014763 |
| 5 | SAS | 0.0023465 | 0.0030116 | 0.0023506 |
| 6 | AFR | 0.0010003 | 0.0014310 | 0.0009608 |
| 6 | AMR | 0.0013976 | 0.0018431 | 0.0013981 |
| 6 | EAS | 0.0024011 | 0.0031797 | 0.0024318 |
| 6 | EUR | 0.0013123 | 0.0017258 | 0.0012665 |
| 6 | SAS | 0.0020679 | 0.0026763 | 0.0020650 |
| 7 | AFR | 0.0013913 | 0.0018807 | 0.0013021 |
| 7 | AMR | 0.0017797 | 0.0022894 | 0.0017757 |
| 7 | EAS | 0.0030445 | 0.0038232 | 0.0030652 |
| 7 | EUR | 0.0017074 | 0.0022170 | 0.0016397 |
| 7 | SAS | 0.0025239 | 0.0032315 | 0.0025031 |
| 8 | AFR | 0.0010952 | 0.0015763 | 0.0010574 |
| 8 | AMR | 0.0016408 | 0.0021809 | 0.0016906 |
| 8 | EAS | 0.0028758 | 0.0037101 | 0.0028902 |
| 8 | EUR | 0.0015261 | 0.0020471 | 0.0015018 |
| 8 | SAS | 0.0022823 | 0.0029429 | 0.0022780 |
| 9 | AFR | 0.0019710 | 0.0024755 | 0.0018571 |
| 9 | AMR | 0.0023622 | 0.0029090 | 0.0023513 |
| 9 | EAS | 0.0039947 | 0.0049926 | 0.0040020 |
| 9 | EUR | 0.0024834 | 0.0030163 | 0.0024100 |
| 9 | SAS | 0.0033491 | 0.0040325 | 0.0032937 |
| 10 | AFR | 0.0013054 | 0.0018014 | 0.0012220 |
| 10 | AMR | 0.0017613 | 0.0023007 | 0.0017395 |
| 10 | EAS | 0.0029666 | 0.0038215 | 0.0030032 |
| 10 | EUR | 0.0017012 | 0.0022140 | 0.0016233 |
| 10 | SAS | 0.0025656 | 0.0033022 | 0.0025487 |
| 11 | AFR | 0.0011327 | 0.0016113 | 0.0010900 |
| 11 | AMR | 0.0016660 | 0.0022169 | 0.0016743 |
| 11 | EAS | 0.0028719 | 0.0037021 | 0.0028828 |
| 11 | EUR | 0.0015605 | 0.0021015 | 0.0015069 |
| 11 | SAS | 0.0024324 | 0.0031835 | 0.0024156 |
| 12 | AFR | 0.0012347 | 0.0016935 | 0.0011711 |
| 12 | AMR | 0.0017109 | 0.0022619 | 0.0017431 |
| 12 | EAS | 0.0030297 | 0.0038845 | 0.0030974 |
| 12 | EUR | 0.0016848 | 0.0022047 | 0.0016367 |
| 12 | SAS | 0.0026850 | 0.0033016 | 0.0027443 |
| 13 | AFR | 0.0012374 | 0.0016608 | 0.0011887 |
| 13 | AMR | 0.0016338 | 0.0021985 | 0.0016718 |
| 13 | EAS | 0.0030470 | 0.0038889 | 0.0030357 |
| 13 | EUR | 0.0016449 | 0.0021782 | 0.0016133 |
| 13 | SAS | 0.0024617 | 0.0032325 | 0.0024994 |
| 14 | AFR | 0.0015135 | 0.0020048 | 0.0014646 |
| 14 | AMR | 0.0020288 | 0.0026707 | 0.0020724 |
| 14 | EAS | 0.0033255 | 0.0042777 | 0.0033896 |
| 14 | EUR | 0.0019515 | 0.0025040 | 0.0019100 |
| 14 | SAS | 0.0028314 | 0.0035589 | 0.0028525 |
| 15 | AFR | 0.0020558 | 0.0026301 | 0.0019531 |
| 15 | AMR | 0.0024911 | 0.0031218 | 0.0025112 |
| 15 | EAS | 0.0042257 | 0.0051794 | 0.0042498 |
| 15 | EUR | 0.0026587 | 0.0032128 | 0.0025716 |
| 15 | SAS | 0.0035765 | 0.0044363 | 0.0036347 |
| 16 | AFR | 0.0018445 | 0.0025092 | 0.0017355 |
| 16 | AMR | 0.0024940 | 0.0031937 | 0.0025249 |
| 16 | EAS | 0.0041844 | 0.0052628 | 0.0042751 |
| 16 | EUR | 0.0023658 | 0.0031430 | 0.0024116 |
| 16 | SAS | 0.0034933 | 0.0042329 | 0.0034969 |
| 17 | AFR | 0.0019400 | 0.0025814 | 0.0018683 |
| 17 | AMR | 0.0025915 | 0.0032833 | 0.0025548 |
| 17 | EAS | 0.0045569 | 0.0055374 | 0.0046059 |
| 17 | EUR | 0.0025843 | 0.0032542 | 0.0025085 |
| 17 | SAS | 0.0037514 | 0.0046797 | 0.0036319 |
| 18 | AFR | 0.0013736 | 0.0018761 | 0.0013308 |
| 18 | AMR | 0.0019493 | 0.0025107 | 0.0019493 |
| 18 | EAS | 0.0034908 | 0.0044029 | 0.0035391 |
| 18 | EUR | 0.0019470 | 0.0025446 | 0.0019378 |
| 18 | SAS | 0.0028371 | 0.0035722 | 0.0028183 |
| 19 | AFR | 0.0019787 | 0.0026070 | 0.0018653 |
| 19 | AMR | 0.0025439 | 0.0031896 | 0.0024700 |
| 19 | EAS | 0.0043873 | 0.0053070 | 0.0043948 |
| 19 | EUR | 0.0025013 | 0.0031173 | 0.0024208 |
| 19 | SAS | 0.0035366 | 0.0042639 | 0.0035355 |
| 20 | AFR | 0.0019127 | 0.0025023 | 0.0017881 |
| 20 | AMR | 0.0026849 | 0.0033720 | 0.0026430 |
| 20 | EAS | 0.0046822 | 0.0055716 | 0.0046542 |
| 20 | EUR | 0.0025032 | 0.0030775 | 0.0024023 |
| 20 | SAS | 0.0036461 | 0.0044155 | 0.0035863 |
| 21 | AFR | 0.0027883 | 0.0032811 | 0.0027103 |
| 21 | AMR | 0.0030047 | 0.0035338 | 0.0030654 |
| 21 | EAS | 0.0044825 | 0.0052999 | 0.0044698 |
| 21 | EUR | 0.0029705 | 0.0035425 | 0.0029284 |
| 21 | SAS | 0.0039422 | 0.0046324 | 0.0039729 |
| 22 | AFR | 0.0030976 | 0.0037686 | 0.0028908 |
| 22 | AMR | 0.0035044 | 0.0041885 | 0.0034282 |
| 22 | EAS | 0.0056296 | 0.0065746 | 0.0054882 |
| 22 | EUR | 0.0035995 | 0.0041890 | 0.0035406 |
| 22 | SAS | 0.0047719 | 0.0055252 | 0.0046662 |
| 23 | AFR | 0.0008880 | 0.0013558 | 0.0007707 |
| 23 | AMR | 0.0012206 | 0.0016760 | 0.0011439 |
| 23 | EAS | 0.0028352 | 0.0036614 | 0.0026536 |
| 23 | EUR | 0.0015108 | 0.0020636 | 0.0013951 |
| 23 | SAS | 0.0020451 | 0.0026914 | 0.0018639 |
df_switches %>%
group_by(chrom) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
geom_point(size=3) +
theme_bw() +
xlab("Chromosome") +
ylab("Switch Rate") +
labs(colour = "Method", shape = "Method") +
scale_colour_brewer(palette = "Set2") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
scale_x_continuous("Chromosome", labels = as.character(unique(df_switches$chrom)), breaks = unique(df_switches$chrom))

df_switches %>%
group_by(chrom, SUPER) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
geom_point(size=2) +
theme_bw() +
ylab("Switch Rate") +
xlab("Chromosome") +
labs(colour = "Population", shape = "Method") +
scale_colour_brewer(palette = "Set1") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
scale_x_continuous("Chromosome", labels = as.character(unique(df_switches$chrom)), breaks = unique(df_switches$chrom))
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

mod_b <- df_switches %>%
select(Beagle, Eagle, SHAPEIT, chrom, pair_id) %>%
{lmerTest::lmer(Beagle ~ factor(chrom) + (1|pair_id), data = . )}
anova(mod_b) %>% broom::tidy()
# A tibble: 1 × 7
term sumsq meansq NumDF DenDF statistic p.value
<chr> <dbl> <dbl> <int> <dbl> <dbl> <dbl>
1 factor(chrom) 0.00490 0.000223 22 9521. 1092. 0
emmeans::emmeans(mod_b, ~ chrom, pbkrtest.limit = 14244) %>% pairs() %>% broom::tidy() %>%
separate(contrast, into = c("chrom1", "chrom2"), sep = " - ") %>%
filter(chrom1 %in% "chrom23" | chrom2 %in% "chrom23") %>%
knitr::kable()
| term | chrom1 | chrom2 | null.value | estimate | std.error | df | statistic | adj.p.value |
|---|---|---|---|---|---|---|---|---|
| chrom | chrom1 | chrom23 | 0 | 0.0002085 | 4.79e-05 | 1997.721 | 4.3518930 | 0.0030782 |
| chrom | chrom2 | chrom23 | 0 | 0.0000862 | 4.79e-05 | 1997.721 | 1.8000017 | 0.9797694 |
| chrom | chrom3 | chrom23 | 0 | -0.0000404 | 4.79e-05 | 1997.721 | -0.8433140 | 0.9999999 |
| chrom | chrom4 | chrom23 | 0 | -0.0001941 | 4.79e-05 | 1997.721 | -4.0528337 | 0.0105070 |
| chrom | chrom5 | chrom23 | 0 | -0.0000454 | 4.79e-05 | 1997.721 | -0.9487342 | 0.9999991 |
| chrom | chrom6 | chrom23 | 0 | -0.0002355 | 4.79e-05 | 1997.721 | -4.9167873 | 0.0002260 |
| chrom | chrom7 | chrom23 | 0 | 0.0001936 | 4.79e-05 | 1997.721 | 4.0408783 | 0.0110090 |
| chrom | chrom8 | chrom23 | 0 | -0.0000234 | 4.79e-05 | 1997.721 | -0.4886566 | 1.0000000 |
| chrom | chrom9 | chrom23 | 0 | 0.0008878 | 4.79e-05 | 1997.721 | 18.5333599 | 0.0000000 |
| chrom | chrom10 | chrom23 | 0 | 0.0001561 | 4.79e-05 | 1997.721 | 3.2595434 | 0.1477995 |
| chrom | chrom11 | chrom23 | 0 | 0.0000217 | 4.79e-05 | 1997.721 | 0.4521216 | 1.0000000 |
| chrom | chrom12 | chrom23 | 0 | 0.0001425 | 4.79e-05 | 1997.721 | 2.9758272 | 0.2947120 |
| chrom | chrom13 | chrom23 | 0 | 0.0000894 | 4.79e-05 | 1997.721 | 1.8659699 | 0.9696929 |
| chrom | chrom14 | chrom23 | 0 | 0.0004115 | 4.79e-05 | 1997.721 | 8.5899605 | 0.0000000 |
| chrom | chrom15 | chrom23 | 0 | 0.0010363 | 4.79e-05 | 1997.721 | 21.6344847 | 0.0000000 |
| chrom | chrom16 | chrom23 | 0 | 0.0008977 | 4.79e-05 | 1997.721 | 18.7400917 | 0.0000000 |
| chrom | chrom17 | chrom23 | 0 | 0.0010716 | 4.79e-05 | 1997.721 | 22.3708948 | 0.0000000 |
| chrom | chrom18 | chrom23 | 0 | 0.0003664 | 4.79e-05 | 1997.721 | 7.6499754 | 0.0000000 |
| chrom | chrom19 | chrom23 | 0 | 0.0010083 | 4.79e-05 | 1997.721 | 21.0494934 | 0.0000000 |
| chrom | chrom20 | chrom23 | 0 | 0.0010694 | 4.79e-05 | 1997.721 | 22.3259912 | 0.0000000 |
| chrom | chrom21 | chrom23 | 0 | 0.0015355 | 4.79e-05 | 1997.721 | 32.0565019 | 0.0000000 |
| chrom | chrom22 | chrom23 | 0 | 0.0021187 | 4.79e-05 | 1997.721 | 44.2305362 | 0.0000000 |
mod_e <- df_switches %>%
select(Beagle, Eagle, SHAPEIT, chrom, pair_id) %>%
{lmerTest::lmer(Eagle ~ factor(chrom) + (1|pair_id), data = . )}
anova(mod_e) %>% broom::tidy()
# A tibble: 1 × 7
term sumsq meansq NumDF DenDF statistic p.value
<chr> <dbl> <dbl> <int> <dbl> <dbl> <dbl>
1 factor(chrom) 0.00571 0.000259 22 9467. 1191. 0
emmeans::emmeans(mod_e, ~ chrom, pbkrtest.limit = 14244) %>% pairs() %>% broom::tidy() %>%
separate(contrast, into = c("chrom1", "chrom2"), sep = " - ") %>%
filter(chrom1 %in% "chrom23" | chrom2 %in% "chrom23") %>%
knitr::kable()
| term | chrom1 | chrom2 | null.value | estimate | std.error | df | statistic | adj.p.value |
|---|---|---|---|---|---|---|---|---|
| chrom | chrom1 | chrom23 | 0 | 0.0002103 | 5.47e-05 | 1900.994 | 3.8420012 | 0.0232835 |
| chrom | chrom2 | chrom23 | 0 | 0.0000999 | 5.47e-05 | 1900.994 | 1.8253984 | 0.9762487 |
| chrom | chrom3 | chrom23 | 0 | -0.0000578 | 5.47e-05 | 1900.994 | -1.0567801 | 0.9999933 |
| chrom | chrom4 | chrom23 | 0 | -0.0002396 | 5.47e-05 | 1900.994 | -4.3775428 | 0.0027624 |
| chrom | chrom5 | chrom23 | 0 | -0.0000844 | 5.47e-05 | 1900.994 | -1.5426689 | 0.9971521 |
| chrom | chrom6 | chrom23 | 0 | -0.0003275 | 5.47e-05 | 1900.994 | -5.9834024 | 0.0000007 |
| chrom | chrom7 | chrom23 | 0 | 0.0001669 | 5.47e-05 | 1900.994 | 3.0495519 | 0.2500202 |
| chrom | chrom8 | chrom23 | 0 | -0.0000439 | 5.47e-05 | 1900.994 | -0.8019284 | 1.0000000 |
| chrom | chrom9 | chrom23 | 0 | 0.0009016 | 5.47e-05 | 1900.994 | 16.4729705 | 0.0000000 |
| chrom | chrom10 | chrom23 | 0 | 0.0001523 | 5.47e-05 | 1900.994 | 2.7819346 | 0.4316661 |
| chrom | chrom11 | chrom23 | 0 | 0.0000187 | 5.47e-05 | 1900.994 | 0.3407932 | 1.0000000 |
| chrom | chrom12 | chrom23 | 0 | 0.0001132 | 5.47e-05 | 1900.994 | 2.0684998 | 0.9146935 |
| chrom | chrom13 | chrom23 | 0 | 0.0000739 | 5.47e-05 | 1900.994 | 1.3500220 | 0.9995989 |
| chrom | chrom14 | chrom23 | 0 | 0.0004467 | 5.47e-05 | 1900.994 | 8.1626972 | 0.0000000 |
| chrom | chrom15 | chrom23 | 0 | 0.0011159 | 5.47e-05 | 1900.994 | 20.3887982 | 0.0000000 |
| chrom | chrom16 | chrom23 | 0 | 0.0010607 | 5.47e-05 | 1900.994 | 19.3807543 | 0.0000000 |
| chrom | chrom17 | chrom23 | 0 | 0.0012209 | 5.47e-05 | 1900.994 | 22.3084662 | 0.0000000 |
| chrom | chrom18 | chrom23 | 0 | 0.0003914 | 5.47e-05 | 1900.994 | 7.1510578 | 0.0000000 |
| chrom | chrom19 | chrom23 | 0 | 0.0010975 | 5.47e-05 | 1900.994 | 20.0531651 | 0.0000000 |
| chrom | chrom20 | chrom23 | 0 | 0.0011501 | 5.47e-05 | 1900.994 | 21.0134809 | 0.0000000 |
| chrom | chrom21 | chrom23 | 0 | 0.0015277 | 5.47e-05 | 1900.994 | 27.9130811 | 0.0000000 |
| chrom | chrom22 | chrom23 | 0 | 0.0022329 | 5.47e-05 | 1900.994 | 40.7981837 | 0.0000000 |
mod_s <- df_switches %>%
select(Beagle, Eagle, SHAPEIT, chrom, pair_id) %>%
{lmerTest::lmer(SHAPEIT ~ factor(chrom) + (1|pair_id), data = . )}
anova(mod_s) %>% broom::tidy()
# A tibble: 1 × 7
term sumsq meansq NumDF DenDF statistic p.value
<chr> <dbl> <dbl> <int> <dbl> <dbl> <dbl>
1 factor(chrom) 0.00457 0.000208 22 9600. 931. 0
emmeans::emmeans(mod_s, ~ chrom, pbkrtest.limit = 14244) %>% pairs() %>% broom::tidy() %>%
separate(contrast, into = c("chrom1", "chrom2"), sep = " - ") %>%
filter(chrom1 %in% "chrom23" | chrom2 %in% "chrom23") %>%
knitr::kable()
| term | chrom1 | chrom2 | null.value | estimate | std.error | df | statistic | adj.p.value |
|---|---|---|---|---|---|---|---|---|
| chrom | chrom1 | chrom23 | 0 | 0.0003083 | 4.84e-05 | 2038.425 | 6.364209 | 0.0000001 |
| chrom | chrom2 | chrom23 | 0 | 0.0001986 | 4.84e-05 | 2038.425 | 4.098871 | 0.0087573 |
| chrom | chrom3 | chrom23 | 0 | 0.0000907 | 4.84e-05 | 2038.425 | 1.871582 | 0.9686901 |
| chrom | chrom4 | chrom23 | 0 | -0.0000682 | 4.84e-05 | 2038.425 | -1.408091 | 0.9992386 |
| chrom | chrom5 | chrom23 | 0 | 0.0000810 | 4.84e-05 | 2038.425 | 1.671210 | 0.9917721 |
| chrom | chrom6 | chrom23 | 0 | -0.0001189 | 4.84e-05 | 2038.425 | -2.455000 | 0.6892273 |
| chrom | chrom7 | chrom23 | 0 | 0.0002849 | 4.84e-05 | 2038.425 | 5.880450 | 0.0000012 |
| chrom | chrom8 | chrom23 | 0 | 0.0001066 | 4.84e-05 | 2038.425 | 2.200602 | 0.8551050 |
| chrom | chrom9 | chrom23 | 0 | 0.0009618 | 4.84e-05 | 2038.425 | 19.852729 | 0.0000000 |
| chrom | chrom10 | chrom23 | 0 | 0.0002460 | 4.84e-05 | 2038.425 | 5.078894 | 0.0000999 |
| chrom | chrom11 | chrom23 | 0 | 0.0001332 | 4.84e-05 | 2038.425 | 2.750074 | 0.4561909 |
| chrom | chrom12 | chrom23 | 0 | 0.0002711 | 4.84e-05 | 2038.425 | 5.596499 | 0.0000062 |
| chrom | chrom13 | chrom23 | 0 | 0.0002147 | 4.84e-05 | 2038.425 | 4.430895 | 0.0021825 |
| chrom | chrom14 | chrom23 | 0 | 0.0005428 | 4.84e-05 | 2038.425 | 11.205324 | 0.0000000 |
| chrom | chrom15 | chrom23 | 0 | 0.0011367 | 4.84e-05 | 2038.425 | 23.464421 | 0.0000000 |
| chrom | chrom16 | chrom23 | 0 | 0.0010223 | 4.84e-05 | 2038.425 | 21.102187 | 0.0000000 |
| chrom | chrom17 | chrom23 | 0 | 0.0011493 | 4.84e-05 | 2038.425 | 23.724210 | 0.0000000 |
| chrom | chrom18 | chrom23 | 0 | 0.0004882 | 4.84e-05 | 2038.425 | 10.076293 | 0.0000000 |
| chrom | chrom19 | chrom23 | 0 | 0.0010746 | 4.84e-05 | 2038.425 | 22.180865 | 0.0000000 |
| chrom | chrom20 | chrom23 | 0 | 0.0011231 | 4.84e-05 | 2038.425 | 23.182437 | 0.0000000 |
| chrom | chrom21 | chrom23 | 0 | 0.0016532 | 4.84e-05 | 2038.425 | 34.124483 | 0.0000000 |
| chrom | chrom22 | chrom23 | 0 | 0.0021245 | 4.84e-05 | 2038.425 | 43.853271 | 0.0000000 |
# Beagle
autosomes <- df_switches %>% filter(chrom < 23) %>% pull(Beagle)
chrX <- df_switches %>% filter(chrom == 23) %>% pull(Beagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 0.000489 0.00219 0.00170 16.5 1.96e-55 1266. 0.000431 0.000547
# ℹ 2 more variables: method <chr>, alternative <chr>
# Eagle
autosomes <- df_switches %>% filter(chrom < 23) %>% pull(Eagle)
chrX <- df_switches %>% filter(chrom == 23) %>% pull(Eagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 0.000510 0.00280 0.00229 14.7 5.10e-45 1230. 0.000442 0.000579
# ℹ 2 more variables: method <chr>, alternative <chr>
# SHAPEIT
autosomes <- df_switches %>% filter(chrom < 23) %>% pull(SHAPEIT)
chrX <- df_switches %>% filter(chrom == 23) %>% pull(SHAPEIT)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 0.000592 0.00216 0.00157 20.4 1.43e-80 1295. 0.000535 0.000649
# ℹ 2 more variables: method <chr>, alternative <chr>
mod_fit <- df_switches %>%
filter(chrom == 1) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)
df_pairwise <- emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
for(i in 2:23){
mod_fit <- df_switches %>%
filter(chrom == i) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
df_anova <- df_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
df_pairwise <- df_pairwise %>% bind_rows({
emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
}
df_anova %>% knitr::kable()
| term | sumsq | meansq | NumDF | DenDF | statistic | p.value | chrom |
|---|---|---|---|---|---|---|---|
| method | 0.0001491 | 0.0000746 | 2 | 1202 | 3681.9647 | 0 | 1 |
| method | 0.0001517 | 0.0000758 | 2 | 1202 | 4198.5629 | 0 | 2 |
| method | 0.0001322 | 0.0000661 | 2 | 1202 | 3641.1256 | 0 | 3 |
| method | 0.0001208 | 0.0000604 | 2 | 1202 | 3592.7161 | 0 | 4 |
| method | 0.0001235 | 0.0000618 | 2 | 1202 | 3082.7573 | 0 | 5 |
| method | 0.0001031 | 0.0000516 | 2 | 1202 | 2828.8144 | 0 | 6 |
| method | 0.0001377 | 0.0000689 | 2 | 1202 | 3275.4743 | 0 | 7 |
| method | 0.0001311 | 0.0000655 | 2 | 1202 | 2834.3344 | 0 | 8 |
| method | 0.0001623 | 0.0000811 | 2 | 1202 | 2145.1325 | 0 | 9 |
| method | 0.0001490 | 0.0000745 | 2 | 1202 | 3192.6028 | 0 | 10 |
| method | 0.0001437 | 0.0000719 | 2 | 1202 | 2794.6550 | 0 | 11 |
| method | 0.0001274 | 0.0000637 | 2 | 1202 | 1211.4197 | 0 | 12 |
| method | 0.0001345 | 0.0000672 | 2 | 1202 | 1955.5305 | 0 | 13 |
| method | 0.0001575 | 0.0000788 | 2 | 1202 | 2029.5949 | 0 | 14 |
| method | 0.0001894 | 0.0000947 | 2 | 1202 | 1776.8041 | 0 | 15 |
| method | 0.0002304 | 0.0001152 | 2 | 1202 | 2021.3109 | 0 | 16 |
| method | 0.0002373 | 0.0001187 | 2 | 1202 | 2081.4072 | 0 | 17 |
| method | 0.0001548 | 0.0000774 | 2 | 1202 | 1772.8476 | 0 | 18 |
| method | 0.0002054 | 0.0001027 | 2 | 1202 | 1771.9228 | 0 | 19 |
| method | 0.0002047 | 0.0001024 | 2 | 1202 | 1744.3432 | 0 | 20 |
| method | 0.0001399 | 0.0000700 | 2 | 1202 | 761.6489 | 0 | 21 |
| method | 0.0002418 | 0.0001209 | 2 | 1202 | 963.2671 | 0 | 22 |
| method | 0.0002968 | 0.0001484 | 2 | 1998 | 4651.3018 | 0 | 23 |
df_pairwise %>% knitr::kable()
| term | contrast | null.value | estimate | std.error | df | statistic | adj.p.value | chrom |
|---|---|---|---|---|---|---|---|---|
| method | Beagle - Eagle | 0 | -0.0005915 | 8.20e-06 | 1202 | -72.1124435 | 0.0000000 | 1 |
| method | Beagle - SHAPEIT | 0 | 0.0000347 | 8.20e-06 | 1202 | 4.2276912 | 0.0000753 | 1 |
| method | Eagle - SHAPEIT | 0 | 0.0006262 | 8.20e-06 | 1202 | 76.3401347 | 0.0000000 | 1 |
| method | Beagle - Eagle | 0 | -0.0006033 | 7.70e-06 | 1202 | -77.8881980 | 0.0000000 | 2 |
| method | Beagle - SHAPEIT | 0 | 0.0000222 | 7.70e-06 | 1202 | 2.8639849 | 0.0118423 | 2 |
| method | Eagle - SHAPEIT | 0 | 0.0006255 | 7.70e-06 | 1202 | 80.7521829 | 0.0000000 | 2 |
| method | Beagle - Eagle | 0 | -0.0005722 | 7.80e-06 | 1202 | -73.6787080 | 0.0000000 | 3 |
| method | Beagle - SHAPEIT | 0 | 0.0000035 | 7.80e-06 | 1202 | 0.4470285 | 0.8957285 | 3 |
| method | Eagle - SHAPEIT | 0 | 0.0005757 | 7.80e-06 | 1202 | 74.1257365 | 0.0000000 | 3 |
| method | Beagle - Eagle | 0 | -0.0005442 | 7.50e-06 | 1202 | -72.8267201 | 0.0000000 | 4 |
| method | Beagle - SHAPEIT | 0 | 0.0000086 | 7.50e-06 | 1202 | 1.1535897 | 0.4813231 | 4 |
| method | Eagle - SHAPEIT | 0 | 0.0005528 | 7.50e-06 | 1202 | 73.9803098 | 0.0000000 | 4 |
| method | Beagle - Eagle | 0 | -0.0005507 | 8.20e-06 | 1202 | -67.4973130 | 0.0000000 | 5 |
| method | Beagle - SHAPEIT | 0 | 0.0000081 | 8.20e-06 | 1202 | 0.9964217 | 0.5792582 | 5 |
| method | Eagle - SHAPEIT | 0 | 0.0005588 | 8.20e-06 | 1202 | 68.4937347 | 0.0000000 | 5 |
| method | Beagle - Eagle | 0 | -0.0004977 | 7.80e-06 | 1202 | -63.9557532 | 0.0000000 | 6 |
| method | Beagle - SHAPEIT | 0 | 0.0000180 | 7.80e-06 | 1202 | 2.3072203 | 0.0551773 | 6 |
| method | Eagle - SHAPEIT | 0 | 0.0005157 | 7.80e-06 | 1202 | 66.2629735 | 0.0000000 | 6 |
| method | Beagle - Eagle | 0 | -0.0005630 | 8.40e-06 | 1202 | -67.3657237 | 0.0000000 | 7 |
| method | Beagle - SHAPEIT | 0 | 0.0000432 | 8.40e-06 | 1202 | 5.1707846 | 0.0000008 | 7 |
| method | Eagle - SHAPEIT | 0 | 0.0006062 | 8.40e-06 | 1202 | 72.5365082 | 0.0000000 | 7 |
| method | Beagle - Eagle | 0 | -0.0005692 | 8.80e-06 | 1202 | -64.9441124 | 0.0000000 | 8 |
| method | Beagle - SHAPEIT | 0 | 0.0000045 | 8.80e-06 | 1202 | 0.5157943 | 0.8636589 | 8 |
| method | Eagle - SHAPEIT | 0 | 0.0005737 | 8.80e-06 | 1202 | 65.4599067 | 0.0000000 | 8 |
| method | Beagle - Eagle | 0 | -0.0006035 | 1.12e-05 | 1202 | -53.8327217 | 0.0000000 | 9 |
| method | Beagle - SHAPEIT | 0 | 0.0000605 | 1.12e-05 | 1202 | 5.3981457 | 0.0000002 | 9 |
| method | Eagle - SHAPEIT | 0 | 0.0006640 | 1.12e-05 | 1202 | 59.2308674 | 0.0000000 | 9 |
| method | Beagle - Eagle | 0 | -0.0005858 | 8.80e-06 | 1202 | -66.5288037 | 0.0000000 | 10 |
| method | Beagle - SHAPEIT | 0 | 0.0000446 | 8.80e-06 | 1202 | 5.0676065 | 0.0000014 | 10 |
| method | Eagle - SHAPEIT | 0 | 0.0006304 | 8.80e-06 | 1202 | 71.5964102 | 0.0000000 | 10 |
| method | Beagle - Eagle | 0 | -0.0005867 | 9.20e-06 | 1202 | -63.4675437 | 0.0000000 | 11 |
| method | Beagle - SHAPEIT | 0 | 0.0000230 | 9.20e-06 | 1202 | 2.4844345 | 0.0349814 | 11 |
| method | Eagle - SHAPEIT | 0 | 0.0006096 | 9.20e-06 | 1202 | 65.9519782 | 0.0000000 | 11 |
| method | Beagle - Eagle | 0 | -0.0005603 | 1.32e-05 | 1202 | -42.4007339 | 0.0000000 | 12 |
| method | Beagle - SHAPEIT | 0 | 0.0000060 | 1.32e-05 | 1202 | 0.4505651 | 0.8941638 | 12 |
| method | Eagle - SHAPEIT | 0 | 0.0005663 | 1.32e-05 | 1202 | 42.8512989 | 0.0000000 | 12 |
| method | Beagle - Eagle | 0 | -0.0005742 | 1.07e-05 | 1202 | -53.7215046 | 0.0000000 | 13 |
| method | Beagle - SHAPEIT | 0 | 0.0000093 | 1.07e-05 | 1202 | 0.8664128 | 0.6616136 | 13 |
| method | Eagle - SHAPEIT | 0 | 0.0005834 | 1.07e-05 | 1202 | 54.5879174 | 0.0000000 | 13 |
| method | Beagle - Eagle | 0 | -0.0006249 | 1.14e-05 | 1202 | -55.0367662 | 0.0000000 | 14 |
| method | Beagle - SHAPEIT | 0 | 0.0000032 | 1.14e-05 | 1202 | 0.2774466 | 0.9584566 | 14 |
| method | Eagle - SHAPEIT | 0 | 0.0006281 | 1.14e-05 | 1202 | 55.3142128 | 0.0000000 | 14 |
| method | Beagle - Eagle | 0 | -0.0006692 | 1.33e-05 | 1202 | -50.2969730 | 0.0000000 | 15 |
| method | Beagle - SHAPEIT | 0 | 0.0000341 | 1.33e-05 | 1202 | 2.5619267 | 0.0283741 | 15 |
| method | Eagle - SHAPEIT | 0 | 0.0007033 | 1.33e-05 | 1202 | 52.8588996 | 0.0000000 | 15 |
| method | Beagle - Eagle | 0 | -0.0007527 | 1.38e-05 | 1202 | -54.7005693 | 0.0000000 | 16 |
| method | Beagle - SHAPEIT | 0 | 0.0000099 | 1.38e-05 | 1202 | 0.7184190 | 0.7526318 | 16 |
| method | Eagle - SHAPEIT | 0 | 0.0007626 | 1.38e-05 | 1202 | 55.4189884 | 0.0000000 | 16 |
| method | Beagle - Eagle | 0 | -0.0007390 | 1.38e-05 | 1202 | -53.6987663 | 0.0000000 | 17 |
| method | Beagle - SHAPEIT | 0 | 0.0000568 | 1.38e-05 | 1202 | 4.1254878 | 0.0001170 | 17 |
| method | Eagle - SHAPEIT | 0 | 0.0007958 | 1.38e-05 | 1202 | 57.8242541 | 0.0000000 | 17 |
| method | Beagle - Eagle | 0 | -0.0006146 | 1.20e-05 | 1202 | -51.0276338 | 0.0000000 | 18 |
| method | Beagle - SHAPEIT | 0 | 0.0000128 | 1.20e-05 | 1202 | 1.0644983 | 0.5363635 | 18 |
| method | Eagle - SHAPEIT | 0 | 0.0006274 | 1.20e-05 | 1202 | 52.0921321 | 0.0000000 | 18 |
| method | Beagle - Eagle | 0 | -0.0006789 | 1.39e-05 | 1202 | -48.9194865 | 0.0000000 | 19 |
| method | Beagle - SHAPEIT | 0 | 0.0000682 | 1.39e-05 | 1202 | 4.9179190 | 0.0000030 | 19 |
| method | Eagle - SHAPEIT | 0 | 0.0007471 | 1.39e-05 | 1202 | 53.8374055 | 0.0000000 | 19 |
| method | Beagle - Eagle | 0 | -0.0006703 | 1.40e-05 | 1202 | -48.0091624 | 0.0000000 | 20 |
| method | Beagle - SHAPEIT | 0 | 0.0000809 | 1.40e-05 | 1202 | 5.7923147 | 0.0000000 | 20 |
| method | Eagle - SHAPEIT | 0 | 0.0007512 | 1.40e-05 | 1202 | 53.8014771 | 0.0000000 | 20 |
| method | Beagle - Eagle | 0 | -0.0005818 | 1.75e-05 | 1202 | -33.3071614 | 0.0000000 | 21 |
| method | Beagle - SHAPEIT | 0 | 0.0000169 | 1.75e-05 | 1202 | 0.9659577 | 0.5985721 | 21 |
| method | Eagle - SHAPEIT | 0 | 0.0005987 | 1.75e-05 | 1202 | 34.2731192 | 0.0000000 | 21 |
| method | Beagle - Eagle | 0 | -0.0007039 | 2.04e-05 | 1202 | -34.4670939 | 0.0000000 | 22 |
| method | Beagle - SHAPEIT | 0 | 0.0001287 | 2.04e-05 | 1202 | 6.3018574 | 0.0000000 | 22 |
| method | Eagle - SHAPEIT | 0 | 0.0008326 | 2.04e-05 | 1202 | 40.7689512 | 0.0000000 | 22 |
| method | Beagle - Eagle | 0 | -0.0005897 | 8.00e-06 | 1998 | -73.8229089 | 0.0000000 | 23 |
| method | Beagle - SHAPEIT | 0 | 0.0001345 | 8.00e-06 | 1998 | 16.8434174 | 0.0000000 | 23 |
| method | Eagle - SHAPEIT | 0 | 0.0007242 | 8.00e-06 | 1998 | 90.6663262 | 0.0000000 | 23 |
Now let’s do these comparisons within each super-population:
mod_fit <- df_switches %>%
filter(chrom == 1) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
df_pop_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)
df_pop_pairwise <- emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
df_pop_pop <- emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = 1)
for(i in 2:23){
mod_fit <- df_switches %>%
filter(chrom == i) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
df_pop_anova <- df_pop_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
df_pop_pairwise <- df_pop_pairwise %>% bind_rows({
emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
df_pop_pop <- df_pop_pop %>% bind_rows({
emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = i)})
}
df_pop_anova %>%
knitr::kable()
| term | sumsq | meansq | NumDF | DenDF | statistic | p.value | chrom |
|---|---|---|---|---|---|---|---|
| method | 0.0001496 | 0.0000748 | 2 | 1194.0000 | 5014.194390 | 0e+00 | 1 |
| SUPER | 0.0000119 | 0.0000030 | 4 | 597.0000 | 198.717719 | 0e+00 | 1 |
| method:SUPER | 0.0000065 | 0.0000008 | 8 | 1194.0000 | 54.685913 | 0e+00 | 1 |
| method | 0.0001496 | 0.0000748 | 2 | 1194.0000 | 5442.934800 | 0e+00 | 2 |
| SUPER | 0.0000107 | 0.0000027 | 4 | 597.0000 | 195.359641 | 0e+00 | 2 |
| method:SUPER | 0.0000053 | 0.0000007 | 8 | 1194.0000 | 48.193179 | 0e+00 | 2 |
| method | 0.0001310 | 0.0000655 | 2 | 1194.0000 | 4748.229364 | 0e+00 | 3 |
| SUPER | 0.0000103 | 0.0000026 | 4 | 597.0000 | 186.224720 | 0e+00 | 3 |
| method:SUPER | 0.0000054 | 0.0000007 | 8 | 1194.0000 | 48.543572 | 0e+00 | 3 |
| method | 0.0001206 | 0.0000603 | 2 | 1194.0000 | 4736.804165 | 0e+00 | 4 |
| SUPER | 0.0000093 | 0.0000023 | 4 | 597.0000 | 182.688205 | 0e+00 | 4 |
| method:SUPER | 0.0000050 | 0.0000006 | 8 | 1194.0000 | 49.047522 | 0e+00 | 4 |
| method | 0.0001233 | 0.0000616 | 2 | 1194.0000 | 3954.352609 | 0e+00 | 5 |
| SUPER | 0.0000112 | 0.0000028 | 4 | 597.0000 | 179.972326 | 0e+00 | 5 |
| method:SUPER | 0.0000055 | 0.0000007 | 8 | 1194.0000 | 43.907671 | 0e+00 | 5 |
| method | 0.0001032 | 0.0000516 | 2 | 1194.0000 | 3663.509419 | 0e+00 | 6 |
| SUPER | 0.0000088 | 0.0000022 | 4 | 597.0000 | 156.487220 | 0e+00 | 6 |
| method:SUPER | 0.0000051 | 0.0000006 | 8 | 1194.0000 | 45.144347 | 0e+00 | 6 |
| method | 0.0001337 | 0.0000668 | 2 | 1194.0000 | 3768.753240 | 0e+00 | 7 |
| SUPER | 0.0000115 | 0.0000029 | 4 | 597.0000 | 161.880271 | 0e+00 | 7 |
| method:SUPER | 0.0000041 | 0.0000005 | 8 | 1194.0000 | 28.879945 | 0e+00 | 7 |
| method | 0.0001302 | 0.0000651 | 2 | 1194.0000 | 3415.028099 | 0e+00 | 8 |
| SUPER | 0.0000135 | 0.0000034 | 4 | 597.0000 | 177.569924 | 0e+00 | 8 |
| method:SUPER | 0.0000050 | 0.0000006 | 8 | 1194.0000 | 33.019615 | 0e+00 | 8 |
| method | 0.0001626 | 0.0000813 | 2 | 1194.0000 | 2648.080634 | 0e+00 | 9 |
| SUPER | 0.0000224 | 0.0000056 | 4 | 597.0000 | 182.298694 | 0e+00 | 9 |
| method:SUPER | 0.0000088 | 0.0000011 | 8 | 1194.0000 | 35.873591 | 0e+00 | 9 |
| method | 0.0001466 | 0.0000733 | 2 | 1194.0001 | 3844.572265 | 0e+00 | 10 |
| SUPER | 0.0000143 | 0.0000036 | 4 | 596.9998 | 187.814753 | 0e+00 | 10 |
| method:SUPER | 0.0000053 | 0.0000007 | 8 | 1194.0001 | 34.614194 | 0e+00 | 10 |
| method | 0.0001444 | 0.0000722 | 2 | 1194.0000 | 3424.093674 | 0e+00 | 11 |
| SUPER | 0.0000146 | 0.0000036 | 4 | 597.0000 | 172.872772 | 0e+00 | 11 |
| method:SUPER | 0.0000057 | 0.0000007 | 8 | 1194.0000 | 34.027636 | 0e+00 | 11 |
| method | 0.0001250 | 0.0000625 | 2 | 1194.0000 | 1281.508285 | 0e+00 | 12 |
| SUPER | 0.0000196 | 0.0000049 | 4 | 597.0000 | 100.644592 | 0e+00 | 12 |
| method:SUPER | 0.0000049 | 0.0000006 | 8 | 1194.0000 | 12.632958 | 0e+00 | 12 |
| method | 0.0001392 | 0.0000696 | 2 | 1194.0000 | 2498.343364 | 0e+00 | 13 |
| SUPER | 0.0000207 | 0.0000052 | 4 | 597.0000 | 185.557054 | 0e+00 | 13 |
| method:SUPER | 0.0000081 | 0.0000010 | 8 | 1194.0000 | 36.167211 | 0e+00 | 13 |
| method | 0.0001579 | 0.0000790 | 2 | 1194.0000 | 2382.681969 | 0e+00 | 14 |
| SUPER | 0.0000190 | 0.0000047 | 4 | 597.0000 | 142.990364 | 0e+00 | 14 |
| method:SUPER | 0.0000071 | 0.0000009 | 8 | 1194.0000 | 26.699004 | 0e+00 | 14 |
| method | 0.0001845 | 0.0000923 | 2 | 1194.0000 | 1932.907282 | 0e+00 | 15 |
| SUPER | 0.0000278 | 0.0000069 | 4 | 597.0000 | 145.522159 | 0e+00 | 15 |
| method:SUPER | 0.0000071 | 0.0000009 | 8 | 1194.0000 | 18.509090 | 0e+00 | 15 |
| method | 0.0002177 | 0.0001088 | 2 | 1194.0000 | 2078.946898 | 0e+00 | 16 |
| SUPER | 0.0000297 | 0.0000074 | 4 | 597.0000 | 141.765615 | 0e+00 | 16 |
| method:SUPER | 0.0000060 | 0.0000007 | 8 | 1194.0000 | 14.308354 | 0e+00 | 16 |
| method | 0.0002308 | 0.0001154 | 2 | 1194.0000 | 2230.086249 | 0e+00 | 17 |
| SUPER | 0.0000338 | 0.0000084 | 4 | 597.0000 | 163.231753 | 0e+00 | 17 |
| method:SUPER | 0.0000067 | 0.0000008 | 8 | 1194.0000 | 16.297216 | 0e+00 | 17 |
| method | 0.0001554 | 0.0000777 | 2 | 1194.0000 | 2002.049963 | 0e+00 | 18 |
| SUPER | 0.0000280 | 0.0000070 | 4 | 597.0000 | 180.156650 | 0e+00 | 18 |
| method:SUPER | 0.0000061 | 0.0000008 | 8 | 1194.0000 | 19.764112 | 0e+00 | 18 |
| method | 0.0001904 | 0.0000952 | 2 | 1194.0000 | 1705.412390 | 0e+00 | 19 |
| SUPER | 0.0000361 | 0.0000090 | 4 | 597.0000 | 161.480118 | 0e+00 | 19 |
| method:SUPER | 0.0000030 | 0.0000004 | 8 | 1194.0000 | 6.764480 | 0e+00 | 19 |
| method | 0.0001931 | 0.0000965 | 2 | 1194.0000 | 1723.663367 | 0e+00 | 20 |
| SUPER | 0.0000365 | 0.0000091 | 4 | 597.0000 | 162.938879 | 0e+00 | 20 |
| method:SUPER | 0.0000037 | 0.0000005 | 8 | 1194.0000 | 8.156113 | 0e+00 | 20 |
| method | 0.0001375 | 0.0000687 | 2 | 1194.0000 | 779.869376 | 0e+00 | 21 |
| SUPER | 0.0000295 | 0.0000074 | 4 | 597.0000 | 83.703338 | 0e+00 | 21 |
| method:SUPER | 0.0000052 | 0.0000006 | 8 | 1194.0000 | 7.321987 | 0e+00 | 21 |
| method | 0.0002223 | 0.0001111 | 2 | 1194.0000 | 915.286997 | 0e+00 | 22 |
| SUPER | 0.0000468 | 0.0000117 | 4 | 597.0000 | 96.401595 | 0e+00 | 22 |
| method:SUPER | 0.0000059 | 0.0000007 | 8 | 1194.0000 | 6.071499 | 1e-07 | 22 |
| method | 0.0002968 | 0.0001484 | 2 | 1990.0001 | 6292.933267 | 0e+00 | 23 |
| SUPER | 0.0000360 | 0.0000090 | 4 | 994.9997 | 382.040973 | 0e+00 | 23 |
| method:SUPER | 0.0000168 | 0.0000021 | 8 | 1990.0001 | 89.146795 | 0e+00 | 23 |
df_pop_pairwise %>% knitr::kable()
| SUPER | term | contrast | null.value | estimate | std.error | df | statistic | adj.p.value | chrom |
|---|---|---|---|---|---|---|---|---|---|
| AFR | method | Beagle - Eagle | 0 | -0.0004848 | 1.22e-05 | 1194 | -39.7886413 | 0.0000000 | 1 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000661 | 1.22e-05 | 1194 | 5.4284702 | 0.0000002 | 1 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005509 | 1.22e-05 | 1194 | 45.2171115 | 0.0000000 | 1 |
| AMR | method | Beagle - Eagle | 0 | -0.0005501 | 1.48e-05 | 1194 | -37.2747818 | 0.0000000 | 1 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000178 | 1.48e-05 | 1194 | 1.2073952 | 0.4489875 | 1 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005679 | 1.48e-05 | 1194 | 38.4821771 | 0.0000000 | 1 |
| EAS | method | Beagle - Eagle | 0 | -0.0009117 | 2.04e-05 | 1194 | -44.7834375 | 0.0000000 | 1 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000324 | 2.04e-05 | 1194 | -1.5938996 | 0.2486367 | 1 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008792 | 2.04e-05 | 1194 | 43.1895380 | 0.0000000 | 1 |
| EUR | method | Beagle - Eagle | 0 | -0.0005309 | 1.67e-05 | 1194 | -31.7907575 | 0.0000000 | 1 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000564 | 1.67e-05 | 1194 | 3.3777776 | 0.0021759 | 1 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005873 | 1.67e-05 | 1194 | 35.1685350 | 0.0000000 | 1 |
| SAS | method | Beagle - Eagle | 0 | -0.0007155 | 1.87e-05 | 1194 | -38.1900539 | 0.0000000 | 1 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000169 | 1.87e-05 | 1194 | 0.9045021 | 0.6375561 | 1 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007325 | 1.87e-05 | 1194 | 39.0945559 | 0.0000000 | 1 |
| AFR | method | Beagle - Eagle | 0 | -0.0005135 | 1.17e-05 | 1194 | -43.9081743 | 0.0000000 | 2 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000462 | 1.17e-05 | 1194 | 3.9533922 | 0.0002405 | 2 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005597 | 1.17e-05 | 1194 | 47.8615665 | 0.0000000 | 2 |
| AMR | method | Beagle - Eagle | 0 | -0.0005781 | 1.42e-05 | 1194 | -40.8112466 | 0.0000000 | 2 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000021 | 1.42e-05 | 1194 | 0.1459337 | 0.9883278 | 2 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005802 | 1.42e-05 | 1194 | 40.9571804 | 0.0000000 | 2 |
| EAS | method | Beagle - Eagle | 0 | -0.0008646 | 1.95e-05 | 1194 | -44.2511853 | 0.0000000 | 2 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000195 | 1.95e-05 | 1194 | -0.9962264 | 0.5793828 | 2 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008452 | 1.95e-05 | 1194 | 43.2549589 | 0.0000000 | 2 |
| EUR | method | Beagle - Eagle | 0 | -0.0005174 | 1.60e-05 | 1194 | -32.2778534 | 0.0000000 | 2 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000417 | 1.60e-05 | 1194 | 2.5993975 | 0.0255885 | 2 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005590 | 1.60e-05 | 1194 | 34.8772509 | 0.0000000 | 2 |
| SAS | method | Beagle - Eagle | 0 | -0.0007434 | 1.80e-05 | 1194 | -41.3411389 | 0.0000000 | 2 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000085 | 1.80e-05 | 1194 | 0.4730133 | 0.8840124 | 2 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007520 | 1.80e-05 | 1194 | 41.8141522 | 0.0000000 | 2 |
| AFR | method | Beagle - Eagle | 0 | -0.0004931 | 1.17e-05 | 1194 | -42.0962550 | 0.0000000 | 3 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000332 | 1.17e-05 | 1194 | 2.8309661 | 0.0130887 | 3 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005263 | 1.17e-05 | 1194 | 44.9272211 | 0.0000000 | 3 |
| AMR | method | Beagle - Eagle | 0 | -0.0005221 | 1.42e-05 | 1194 | -36.7974736 | 0.0000000 | 3 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000014 | 1.42e-05 | 1194 | -0.0967627 | 0.9948513 | 3 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005208 | 1.42e-05 | 1194 | 36.7007109 | 0.0000000 | 3 |
| EAS | method | Beagle - Eagle | 0 | -0.0008802 | 1.96e-05 | 1194 | -44.9693004 | 0.0000000 | 3 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000600 | 1.96e-05 | 1194 | -3.0639246 | 0.0063175 | 3 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008202 | 1.96e-05 | 1194 | 41.9053758 | 0.0000000 | 3 |
| EUR | method | Beagle - Eagle | 0 | -0.0005040 | 1.61e-05 | 1194 | -31.3906136 | 0.0000000 | 3 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000200 | 1.61e-05 | 1194 | 1.2430270 | 0.4280413 | 3 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005240 | 1.61e-05 | 1194 | 32.6336406 | 0.0000000 | 3 |
| SAS | method | Beagle - Eagle | 0 | -0.0006650 | 1.80e-05 | 1194 | -36.9150451 | 0.0000000 | 3 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0000259 | 1.80e-05 | 1194 | -1.4402671 | 0.3205575 | 3 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0006390 | 1.80e-05 | 1194 | 35.4747780 | 0.0000000 | 3 |
| AFR | method | Beagle - Eagle | 0 | -0.0004339 | 1.13e-05 | 1194 | -38.5466075 | 0.0000000 | 4 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000511 | 1.13e-05 | 1194 | 4.5354027 | 0.0000189 | 4 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0004850 | 1.13e-05 | 1194 | 43.0820103 | 0.0000000 | 4 |
| AMR | method | Beagle - Eagle | 0 | -0.0005228 | 1.36e-05 | 1194 | -38.3434378 | 0.0000000 | 4 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000083 | 1.36e-05 | 1194 | -0.6119203 | 0.8136340 | 4 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005145 | 1.36e-05 | 1194 | 37.7315175 | 0.0000000 | 4 |
| EAS | method | Beagle - Eagle | 0 | -0.0008400 | 1.88e-05 | 1194 | -44.6613885 | 0.0000000 | 4 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000973 | 1.88e-05 | 1194 | -5.1753282 | 0.0000008 | 4 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0007427 | 1.88e-05 | 1194 | 39.4860602 | 0.0000000 | 4 |
| EUR | method | Beagle - Eagle | 0 | -0.0005122 | 1.54e-05 | 1194 | -33.1984219 | 0.0000000 | 4 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000316 | 1.54e-05 | 1194 | 2.0483651 | 0.1013175 | 4 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005438 | 1.54e-05 | 1194 | 35.2467870 | 0.0000000 | 4 |
| SAS | method | Beagle - Eagle | 0 | -0.0006292 | 1.73e-05 | 1194 | -36.3475660 | 0.0000000 | 4 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0000036 | 1.73e-05 | 1194 | -0.2056646 | 0.9769522 | 4 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0006256 | 1.73e-05 | 1194 | 36.1419015 | 0.0000000 | 4 |
| AFR | method | Beagle - Eagle | 0 | -0.0004639 | 1.25e-05 | 1194 | -37.2522381 | 0.0000000 | 5 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000540 | 1.25e-05 | 1194 | 4.3384791 | 0.0000462 | 5 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005179 | 1.25e-05 | 1194 | 41.5907172 | 0.0000000 | 5 |
| AMR | method | Beagle - Eagle | 0 | -0.0005029 | 1.51e-05 | 1194 | -33.3397329 | 0.0000000 | 5 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000430 | 1.51e-05 | 1194 | -2.8510091 | 0.0123197 | 5 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0004599 | 1.51e-05 | 1194 | 30.4887238 | 0.0000000 | 5 |
| EAS | method | Beagle - Eagle | 0 | -0.0008289 | 2.08e-05 | 1194 | -39.8393654 | 0.0000000 | 5 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000365 | 2.08e-05 | 1194 | -1.7549461 | 0.1854418 | 5 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0007924 | 2.08e-05 | 1194 | 38.0844193 | 0.0000000 | 5 |
| EUR | method | Beagle - Eagle | 0 | -0.0004968 | 1.71e-05 | 1194 | -29.1088093 | 0.0000000 | 5 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000271 | 1.71e-05 | 1194 | 1.5904161 | 0.2501429 | 5 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005240 | 1.71e-05 | 1194 | 30.6992255 | 0.0000000 | 5 |
| SAS | method | Beagle - Eagle | 0 | -0.0006651 | 1.91e-05 | 1194 | -34.7312289 | 0.0000000 | 5 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0000041 | 1.91e-05 | 1194 | -0.2146232 | 0.9749268 | 5 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0006610 | 1.91e-05 | 1194 | 34.5166057 | 0.0000000 | 5 |
| AFR | method | Beagle - Eagle | 0 | -0.0004307 | 1.18e-05 | 1194 | -36.3778360 | 0.0000000 | 6 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000395 | 1.18e-05 | 1194 | 3.3358343 | 0.0025230 | 6 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0004702 | 1.18e-05 | 1194 | 39.7136703 | 0.0000000 | 6 |
| AMR | method | Beagle - Eagle | 0 | -0.0004455 | 1.43e-05 | 1194 | -31.0634768 | 0.0000000 | 6 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000004 | 1.43e-05 | 1194 | -0.0313327 | 0.9994589 | 6 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0004450 | 1.43e-05 | 1194 | 31.0321440 | 0.0000000 | 6 |
| EAS | method | Beagle - Eagle | 0 | -0.0007786 | 1.98e-05 | 1194 | -39.3551654 | 0.0000000 | 6 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000307 | 1.98e-05 | 1194 | -1.5516019 | 0.2673213 | 6 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0007479 | 1.98e-05 | 1194 | 37.8035635 | 0.0000000 | 6 |
| EUR | method | Beagle - Eagle | 0 | -0.0004135 | 1.62e-05 | 1194 | -25.4785216 | 0.0000000 | 6 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000458 | 1.62e-05 | 1194 | 2.8216635 | 0.0134599 | 6 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0004593 | 1.62e-05 | 1194 | 28.3001851 | 0.0000000 | 6 |
| SAS | method | Beagle - Eagle | 0 | -0.0006084 | 1.82e-05 | 1194 | -33.4147698 | 0.0000000 | 6 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000028 | 1.82e-05 | 1194 | 0.1563964 | 0.9866059 | 6 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0006112 | 1.82e-05 | 1194 | 33.5711662 | 0.0000000 | 6 |
| AFR | method | Beagle - Eagle | 0 | -0.0004893 | 1.33e-05 | 1194 | -36.8384796 | 0.0000000 | 7 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000892 | 1.33e-05 | 1194 | 6.7173393 | 0.0000000 | 7 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005786 | 1.33e-05 | 1194 | 43.5558189 | 0.0000000 | 7 |
| AMR | method | Beagle - Eagle | 0 | -0.0005097 | 1.61e-05 | 1194 | -31.6815991 | 0.0000000 | 7 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000040 | 1.61e-05 | 1194 | 0.2492418 | 0.9663358 | 7 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005138 | 1.61e-05 | 1194 | 31.9308409 | 0.0000000 | 7 |
| EAS | method | Beagle - Eagle | 0 | -0.0007787 | 2.22e-05 | 1194 | -35.0853954 | 0.0000000 | 7 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000207 | 2.22e-05 | 1194 | -0.9311449 | 0.6206665 | 7 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0007580 | 2.22e-05 | 1194 | 34.1542505 | 0.0000000 | 7 |
| EUR | method | Beagle - Eagle | 0 | -0.0005095 | 1.82e-05 | 1194 | -27.9878866 | 0.0000000 | 7 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000678 | 1.82e-05 | 1194 | 3.7233301 | 0.0006025 | 7 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005773 | 1.82e-05 | 1194 | 31.7112167 | 0.0000000 | 7 |
| SAS | method | Beagle - Eagle | 0 | -0.0007076 | 2.04e-05 | 1194 | -34.6411363 | 0.0000000 | 7 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000208 | 2.04e-05 | 1194 | 1.0166939 | 0.5664368 | 7 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007284 | 2.04e-05 | 1194 | 35.6578302 | 0.0000000 | 7 |
| AFR | method | Beagle - Eagle | 0 | -0.0004810 | 1.38e-05 | 1194 | -34.9313325 | 0.0000000 | 8 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000378 | 1.38e-05 | 1194 | 2.7462505 | 0.0168314 | 8 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005188 | 1.38e-05 | 1194 | 37.6775830 | 0.0000000 | 8 |
| AMR | method | Beagle - Eagle | 0 | -0.0005401 | 1.67e-05 | 1194 | -32.3807908 | 0.0000000 | 8 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000497 | 1.67e-05 | 1194 | -2.9810694 | 0.0082364 | 8 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0004904 | 1.67e-05 | 1194 | 29.3997213 | 0.0000000 | 8 |
| EAS | method | Beagle - Eagle | 0 | -0.0008343 | 2.30e-05 | 1194 | -36.2603564 | 0.0000000 | 8 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000144 | 2.30e-05 | 1194 | -0.6280035 | 0.8047548 | 8 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008198 | 2.30e-05 | 1194 | 35.6323529 | 0.0000000 | 8 |
| EUR | method | Beagle - Eagle | 0 | -0.0005210 | 1.89e-05 | 1194 | -27.6024083 | 0.0000000 | 8 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000243 | 1.89e-05 | 1194 | 1.2881028 | 0.4021488 | 8 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005453 | 1.89e-05 | 1194 | 28.8905111 | 0.0000000 | 8 |
| SAS | method | Beagle - Eagle | 0 | -0.0006606 | 2.12e-05 | 1194 | -31.1944125 | 0.0000000 | 8 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000044 | 2.12e-05 | 1194 | 0.2061953 | 0.9768345 | 8 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0006649 | 2.12e-05 | 1194 | 31.4006078 | 0.0000000 | 8 |
| AFR | method | Beagle - Eagle | 0 | -0.0005045 | 1.75e-05 | 1194 | -28.8649690 | 0.0000000 | 9 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0001140 | 1.75e-05 | 1194 | 6.5198154 | 0.0000000 | 9 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0006184 | 1.75e-05 | 1194 | 35.3847844 | 0.0000000 | 9 |
| AMR | method | Beagle - Eagle | 0 | -0.0005468 | 2.12e-05 | 1194 | -25.8310397 | 0.0000000 | 9 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000109 | 2.12e-05 | 1194 | 0.5147044 | 0.8641932 | 9 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005577 | 2.12e-05 | 1194 | 26.3457440 | 0.0000000 | 9 |
| EAS | method | Beagle - Eagle | 0 | -0.0009980 | 2.92e-05 | 1194 | -34.1746912 | 0.0000000 | 9 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000074 | 2.92e-05 | 1194 | -0.2519426 | 0.9656152 | 9 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0009906 | 2.92e-05 | 1194 | 33.9227487 | 0.0000000 | 9 |
| EUR | method | Beagle - Eagle | 0 | -0.0005329 | 2.40e-05 | 1194 | -22.2458905 | 0.0000000 | 9 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000734 | 2.40e-05 | 1194 | 3.0634042 | 0.0063281 | 9 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0006063 | 2.40e-05 | 1194 | 25.3092947 | 0.0000000 | 9 |
| SAS | method | Beagle - Eagle | 0 | -0.0006835 | 2.69e-05 | 1194 | -25.4290604 | 0.0000000 | 9 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000554 | 2.69e-05 | 1194 | 2.0616579 | 0.0983708 | 9 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007389 | 2.69e-05 | 1194 | 27.4907183 | 0.0000000 | 9 |
| AFR | method | Beagle - Eagle | 0 | -0.0004960 | 1.38e-05 | 1194 | -36.0113241 | 0.0000000 | 10 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000833 | 1.38e-05 | 1194 | 6.0491303 | 0.0000000 | 10 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005794 | 1.38e-05 | 1194 | 42.0604544 | 0.0000000 | 10 |
| AMR | method | Beagle - Eagle | 0 | -0.0005394 | 1.67e-05 | 1194 | -32.3266164 | 0.0000000 | 10 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000218 | 1.67e-05 | 1194 | 1.3065352 | 0.3917706 | 10 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005612 | 1.67e-05 | 1194 | 33.6331516 | 0.0000000 | 10 |
| EAS | method | Beagle - Eagle | 0 | -0.0008549 | 2.30e-05 | 1194 | -37.1449908 | 0.0000000 | 10 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000366 | 2.30e-05 | 1194 | -1.5921365 | 0.2493983 | 10 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008183 | 2.30e-05 | 1194 | 35.5528544 | 0.0000000 | 10 |
| EUR | method | Beagle - Eagle | 0 | -0.0005128 | 1.89e-05 | 1194 | -27.1635173 | 0.0000000 | 10 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000779 | 1.89e-05 | 1194 | 4.1255422 | 0.0001171 | 10 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005907 | 1.89e-05 | 1194 | 31.2890596 | 0.0000000 | 10 |
| SAS | method | Beagle - Eagle | 0 | -0.0007367 | 2.12e-05 | 1194 | -34.7767915 | 0.0000000 | 10 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000168 | 2.12e-05 | 1194 | 0.7945323 | 0.7064651 | 10 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007535 | 2.12e-05 | 1194 | 35.5713237 | 0.0000000 | 10 |
| AFR | method | Beagle - Eagle | 0 | -0.0004786 | 1.45e-05 | 1194 | -33.0405727 | 0.0000000 | 11 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000427 | 1.45e-05 | 1194 | 2.9501043 | 0.0090788 | 11 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005213 | 1.45e-05 | 1194 | 35.9906770 | 0.0000000 | 11 |
| AMR | method | Beagle - Eagle | 0 | -0.0005509 | 1.75e-05 | 1194 | -31.4030766 | 0.0000000 | 11 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000083 | 1.75e-05 | 1194 | -0.4738340 | 0.8836342 | 11 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005426 | 1.75e-05 | 1194 | 30.9292426 | 0.0000000 | 11 |
| EAS | method | Beagle - Eagle | 0 | -0.0008302 | 2.42e-05 | 1194 | -34.3054548 | 0.0000000 | 11 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000109 | 2.42e-05 | 1194 | -0.4506925 | 0.8941073 | 11 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008193 | 2.42e-05 | 1194 | 33.8547623 | 0.0000000 | 11 |
| EUR | method | Beagle - Eagle | 0 | -0.0005410 | 1.99e-05 | 1194 | -27.2504504 | 0.0000000 | 11 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000536 | 1.99e-05 | 1194 | 2.6978328 | 0.0193706 | 11 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005945 | 1.99e-05 | 1194 | 29.9482832 | 0.0000000 | 11 |
| SAS | method | Beagle - Eagle | 0 | -0.0007511 | 2.23e-05 | 1194 | -33.7229615 | 0.0000000 | 11 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000168 | 2.23e-05 | 1194 | 0.7552775 | 0.7304877 | 11 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007679 | 2.23e-05 | 1194 | 34.4782391 | 0.0000000 | 11 |
| AFR | method | Beagle - Eagle | 0 | -0.0004589 | 2.20e-05 | 1194 | -20.8256958 | 0.0000000 | 12 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000635 | 2.20e-05 | 1194 | 2.8832788 | 0.0111659 | 12 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005224 | 2.20e-05 | 1194 | 23.7089746 | 0.0000000 | 12 |
| AMR | method | Beagle - Eagle | 0 | -0.0005511 | 2.67e-05 | 1194 | -20.6483653 | 0.0000000 | 12 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000322 | 2.67e-05 | 1194 | -1.2069318 | 0.4492626 | 12 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005188 | 2.67e-05 | 1194 | 19.4414335 | 0.0000000 | 12 |
| EAS | method | Beagle - Eagle | 0 | -0.0008548 | 3.68e-05 | 1194 | -23.2202870 | 0.0000000 | 12 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000677 | 3.68e-05 | 1194 | -1.8391891 | 0.1573432 | 12 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0007871 | 3.68e-05 | 1194 | 21.3810979 | 0.0000000 | 12 |
| EUR | method | Beagle - Eagle | 0 | -0.0005199 | 3.02e-05 | 1194 | -17.2168144 | 0.0000000 | 12 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000481 | 3.02e-05 | 1194 | 1.5921232 | 0.2494040 | 12 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005680 | 3.02e-05 | 1194 | 18.8089376 | 0.0000000 | 12 |
| SAS | method | Beagle - Eagle | 0 | -0.0006166 | 3.39e-05 | 1194 | -18.1996848 | 0.0000000 | 12 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0000593 | 3.39e-05 | 1194 | -1.7505059 | 0.1870160 | 12 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0005573 | 3.39e-05 | 1194 | 16.4491788 | 0.0000000 | 12 |
| AFR | method | Beagle - Eagle | 0 | -0.0004233 | 1.67e-05 | 1194 | -25.4238689 | 0.0000000 | 13 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000487 | 1.67e-05 | 1194 | 2.9265783 | 0.0097698 | 13 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0004720 | 1.67e-05 | 1194 | 28.3504472 | 0.0000000 | 13 |
| AMR | method | Beagle - Eagle | 0 | -0.0005647 | 2.02e-05 | 1194 | -28.0014711 | 0.0000000 | 13 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000380 | 2.02e-05 | 1194 | -1.8847916 | 0.1435052 | 13 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005267 | 2.02e-05 | 1194 | 26.1166794 | 0.0000000 | 13 |
| EAS | method | Beagle - Eagle | 0 | -0.0008419 | 2.78e-05 | 1194 | -30.2609517 | 0.0000000 | 13 |
| EAS | method | Beagle - SHAPEIT | 0 | 0.0000113 | 2.78e-05 | 1194 | 0.4072950 | 0.9126339 | 13 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008532 | 2.78e-05 | 1194 | 30.6682467 | 0.0000000 | 13 |
| EUR | method | Beagle - Eagle | 0 | -0.0005333 | 2.28e-05 | 1194 | -23.3693402 | 0.0000000 | 13 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000316 | 2.28e-05 | 1194 | 1.3833907 | 0.3499278 | 13 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005649 | 2.28e-05 | 1194 | 24.7527310 | 0.0000000 | 13 |
| SAS | method | Beagle - Eagle | 0 | -0.0007708 | 2.56e-05 | 1194 | -30.1039942 | 0.0000000 | 13 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0000377 | 2.56e-05 | 1194 | -1.4730930 | 0.3042626 | 13 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007331 | 2.56e-05 | 1194 | 28.6309012 | 0.0000000 | 13 |
| AFR | method | Beagle - Eagle | 0 | -0.0004913 | 1.82e-05 | 1194 | -27.0560426 | 0.0000000 | 14 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000489 | 1.82e-05 | 1194 | 2.6920504 | 0.0196953 | 14 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005402 | 1.82e-05 | 1194 | 29.7480930 | 0.0000000 | 14 |
| AMR | method | Beagle - Eagle | 0 | -0.0006419 | 2.20e-05 | 1194 | -29.1847896 | 0.0000000 | 14 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000436 | 2.20e-05 | 1194 | -1.9799300 | 0.1176013 | 14 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005984 | 2.20e-05 | 1194 | 27.2048596 | 0.0000000 | 14 |
| EAS | method | Beagle - Eagle | 0 | -0.0009522 | 3.03e-05 | 1194 | -31.3846202 | 0.0000000 | 14 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000641 | 3.03e-05 | 1194 | -2.1128677 | 0.0876476 | 14 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008881 | 3.03e-05 | 1194 | 29.2717525 | 0.0000000 | 14 |
| EUR | method | Beagle - Eagle | 0 | -0.0005525 | 2.49e-05 | 1194 | -22.1987473 | 0.0000000 | 14 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000416 | 2.49e-05 | 1194 | 1.6694587 | 0.2174190 | 14 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0005941 | 2.49e-05 | 1194 | 23.8682061 | 0.0000000 | 14 |
| SAS | method | Beagle - Eagle | 0 | -0.0007275 | 2.79e-05 | 1194 | -26.0506668 | 0.0000000 | 14 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0000211 | 2.79e-05 | 1194 | -0.7555807 | 0.7303038 | 14 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007064 | 2.79e-05 | 1194 | 25.2950861 | 0.0000000 | 14 |
| AFR | method | Beagle - Eagle | 0 | -0.0005743 | 2.18e-05 | 1194 | -26.3535930 | 0.0000000 | 15 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0001027 | 2.18e-05 | 1194 | 4.7125204 | 0.0000082 | 15 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0006770 | 2.18e-05 | 1194 | 31.0661134 | 0.0000000 | 15 |
| AMR | method | Beagle - Eagle | 0 | -0.0006306 | 2.64e-05 | 1194 | -23.8908757 | 0.0000000 | 15 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000201 | 2.64e-05 | 1194 | -0.7612565 | 0.7268558 | 15 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0006105 | 2.64e-05 | 1194 | 23.1296193 | 0.0000000 | 15 |
| EAS | method | Beagle - Eagle | 0 | -0.0009537 | 3.64e-05 | 1194 | -26.1926143 | 0.0000000 | 15 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000241 | 3.64e-05 | 1194 | -0.6622936 | 0.7854026 | 15 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0009296 | 3.64e-05 | 1194 | 25.5303207 | 0.0000000 | 15 |
| EUR | method | Beagle - Eagle | 0 | -0.0005542 | 2.99e-05 | 1194 | -18.5541847 | 0.0000000 | 15 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000871 | 2.99e-05 | 1194 | 2.9145756 | 0.0101402 | 15 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0006412 | 2.99e-05 | 1194 | 21.4687603 | 0.0000000 | 15 |
| SAS | method | Beagle - Eagle | 0 | -0.0008598 | 3.35e-05 | 1194 | -25.6579923 | 0.0000000 | 15 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0000582 | 3.35e-05 | 1194 | -1.7365068 | 0.1920409 | 15 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0008016 | 3.35e-05 | 1194 | 23.9214854 | 0.0000000 | 15 |
| AFR | method | Beagle - Eagle | 0 | -0.0006647 | 2.28e-05 | 1194 | -29.1210527 | 0.0000000 | 16 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0001090 | 2.28e-05 | 1194 | 4.7765912 | 0.0000060 | 16 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0007737 | 2.28e-05 | 1194 | 33.8976439 | 0.0000000 | 16 |
| AMR | method | Beagle - Eagle | 0 | -0.0006997 | 2.76e-05 | 1194 | -25.3092022 | 0.0000000 | 16 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000309 | 2.76e-05 | 1194 | -1.1176813 | 0.5033142 | 16 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0006688 | 2.76e-05 | 1194 | 24.1915209 | 0.0000000 | 16 |
| EAS | method | Beagle - Eagle | 0 | -0.0010784 | 3.81e-05 | 1194 | -28.2773994 | 0.0000000 | 16 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000907 | 3.81e-05 | 1194 | -2.3774503 | 0.0462395 | 16 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0009877 | 3.81e-05 | 1194 | 25.8999491 | 0.0000000 | 16 |
| EUR | method | Beagle - Eagle | 0 | -0.0007772 | 3.13e-05 | 1194 | -24.8432150 | 0.0000000 | 16 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0000458 | 3.13e-05 | 1194 | -1.4641268 | 0.3086647 | 16 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0007314 | 3.13e-05 | 1194 | 23.3790882 | 0.0000000 | 16 |
| SAS | method | Beagle - Eagle | 0 | -0.0007396 | 3.51e-05 | 1194 | -21.0718950 | 0.0000000 | 16 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0000035 | 3.51e-05 | 1194 | -0.1006958 | 0.9944255 | 16 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007361 | 3.51e-05 | 1194 | 20.9711992 | 0.0000000 | 16 |
| AFR | method | Beagle - Eagle | 0 | -0.0006415 | 2.27e-05 | 1194 | -28.2696810 | 0.0000000 | 17 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000717 | 2.27e-05 | 1194 | 3.1609305 | 0.0045913 | 17 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0007132 | 2.27e-05 | 1194 | 31.4306115 | 0.0000000 | 17 |
| AMR | method | Beagle - Eagle | 0 | -0.0006918 | 2.75e-05 | 1194 | -25.1708871 | 0.0000000 | 17 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000367 | 2.75e-05 | 1194 | 1.3359853 | 0.3754574 | 17 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0007285 | 2.75e-05 | 1194 | 26.5068724 | 0.0000000 | 17 |
| EAS | method | Beagle - Eagle | 0 | -0.0009805 | 3.79e-05 | 1194 | -25.8636477 | 0.0000000 | 17 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000490 | 3.79e-05 | 1194 | -1.2933483 | 0.3991825 | 17 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0009315 | 3.79e-05 | 1194 | 24.5702994 | 0.0000000 | 17 |
| EUR | method | Beagle - Eagle | 0 | -0.0006699 | 3.11e-05 | 1194 | -21.5413492 | 0.0000000 | 17 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000758 | 3.11e-05 | 1194 | 2.4366683 | 0.0396808 | 17 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0007457 | 3.11e-05 | 1194 | 23.9780175 | 0.0000000 | 17 |
| SAS | method | Beagle - Eagle | 0 | -0.0009283 | 3.49e-05 | 1194 | -26.6049770 | 0.0000000 | 17 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0001195 | 3.49e-05 | 1194 | 3.4239965 | 0.0018447 | 17 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0010478 | 3.49e-05 | 1194 | 30.0289735 | 0.0000000 | 17 |
| AFR | method | Beagle - Eagle | 0 | -0.0005025 | 1.97e-05 | 1194 | -25.5658666 | 0.0000000 | 18 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000428 | 1.97e-05 | 1194 | 2.1777036 | 0.0754366 | 18 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005453 | 1.97e-05 | 1194 | 27.7435702 | 0.0000000 | 18 |
| AMR | method | Beagle - Eagle | 0 | -0.0005614 | 2.38e-05 | 1194 | -23.5813399 | 0.0000000 | 18 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000000 | 2.38e-05 | 1194 | 0.0002905 | 1.0000000 | 18 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005614 | 2.38e-05 | 1194 | 23.5816303 | 0.0000000 | 18 |
| EAS | method | Beagle - Eagle | 0 | -0.0009121 | 3.28e-05 | 1194 | -27.7759201 | 0.0000000 | 18 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000483 | 3.28e-05 | 1194 | -1.4697483 | 0.3059004 | 18 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008638 | 3.28e-05 | 1194 | 26.3061718 | 0.0000000 | 18 |
| EUR | method | Beagle - Eagle | 0 | -0.0005976 | 2.69e-05 | 1194 | -22.1846501 | 0.0000000 | 18 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000092 | 2.69e-05 | 1194 | 0.3427056 | 0.9373182 | 18 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0006068 | 2.69e-05 | 1194 | 22.5273557 | 0.0000000 | 18 |
| SAS | method | Beagle - Eagle | 0 | -0.0007351 | 3.02e-05 | 1194 | -24.3222096 | 0.0000000 | 18 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000188 | 3.02e-05 | 1194 | 0.6236429 | 0.8071752 | 18 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007539 | 3.02e-05 | 1194 | 24.9458524 | 0.0000000 | 18 |
| AFR | method | Beagle - Eagle | 0 | -0.0006283 | 2.36e-05 | 1194 | -26.6582969 | 0.0000000 | 19 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0001134 | 2.36e-05 | 1194 | 4.8108655 | 0.0000051 | 19 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0007417 | 2.36e-05 | 1194 | 31.4691625 | 0.0000000 | 19 |
| AMR | method | Beagle - Eagle | 0 | -0.0006456 | 2.85e-05 | 1194 | -22.6150649 | 0.0000000 | 19 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000739 | 2.85e-05 | 1194 | 2.5897748 | 0.0262807 | 19 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0007196 | 2.85e-05 | 1194 | 25.2048397 | 0.0000000 | 19 |
| EAS | method | Beagle - Eagle | 0 | -0.0009197 | 3.94e-05 | 1194 | -23.3544515 | 0.0000000 | 19 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0000075 | 3.94e-05 | 1194 | -0.1904170 | 0.9802099 | 19 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0009122 | 3.94e-05 | 1194 | 23.1640345 | 0.0000000 | 19 |
| EUR | method | Beagle - Eagle | 0 | -0.0006161 | 3.23e-05 | 1194 | -19.0712235 | 0.0000000 | 19 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000805 | 3.23e-05 | 1194 | 2.4910241 | 0.0343744 | 19 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0006965 | 3.23e-05 | 1194 | 21.5622476 | 0.0000000 | 19 |
| SAS | method | Beagle - Eagle | 0 | -0.0007272 | 3.62e-05 | 1194 | -20.0648596 | 0.0000000 | 19 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000011 | 3.62e-05 | 1194 | 0.0311845 | 0.9994640 | 19 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0007284 | 3.62e-05 | 1194 | 20.0960441 | 0.0000000 | 19 |
| AFR | method | Beagle - Eagle | 0 | -0.0005896 | 2.36e-05 | 1194 | -24.9757304 | 0.0000000 | 20 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0001246 | 2.36e-05 | 1194 | 5.2772216 | 0.0000005 | 20 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0007142 | 2.36e-05 | 1194 | 30.2529520 | 0.0000000 | 20 |
| AMR | method | Beagle - Eagle | 0 | -0.0006870 | 2.86e-05 | 1194 | -24.0269211 | 0.0000000 | 20 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000420 | 2.86e-05 | 1194 | 1.4674466 | 0.3070305 | 20 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0007290 | 2.86e-05 | 1194 | 25.4943677 | 0.0000000 | 20 |
| EAS | method | Beagle - Eagle | 0 | -0.0008894 | 3.94e-05 | 1194 | -22.5494096 | 0.0000000 | 20 |
| EAS | method | Beagle - SHAPEIT | 0 | 0.0000280 | 3.94e-05 | 1194 | 0.7087858 | 0.7583438 | 20 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0009174 | 3.94e-05 | 1194 | 23.2581954 | 0.0000000 | 20 |
| EUR | method | Beagle - Eagle | 0 | -0.0005743 | 3.24e-05 | 1194 | -17.7501488 | 0.0000000 | 20 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0001009 | 3.24e-05 | 1194 | 3.1198495 | 0.0052617 | 20 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0006753 | 3.24e-05 | 1194 | 20.8699983 | 0.0000000 | 20 |
| SAS | method | Beagle - Eagle | 0 | -0.0007694 | 3.63e-05 | 1194 | -21.1936667 | 0.0000000 | 20 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0000598 | 3.63e-05 | 1194 | 1.6469038 | 0.2264468 | 20 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0008292 | 3.63e-05 | 1194 | 22.8405705 | 0.0000000 | 20 |
| AFR | method | Beagle - Eagle | 0 | -0.0004929 | 2.96e-05 | 1194 | -16.6421645 | 0.0000000 | 21 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0000780 | 2.96e-05 | 1194 | 2.6323872 | 0.0233345 | 21 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005708 | 2.96e-05 | 1194 | 19.2745517 | 0.0000000 | 21 |
| AMR | method | Beagle - Eagle | 0 | -0.0005291 | 3.59e-05 | 1194 | -14.7486978 | 0.0000000 | 21 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0000607 | 3.59e-05 | 1194 | -1.6918263 | 0.2087106 | 21 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0004684 | 3.59e-05 | 1194 | 13.0568715 | 0.0000000 | 21 |
| EAS | method | Beagle - Eagle | 0 | -0.0008174 | 4.95e-05 | 1194 | -16.5191428 | 0.0000000 | 21 |
| EAS | method | Beagle - SHAPEIT | 0 | 0.0000127 | 4.95e-05 | 1194 | 0.2563844 | 0.9644143 | 21 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0008301 | 4.95e-05 | 1194 | 16.7755272 | 0.0000000 | 21 |
| EUR | method | Beagle - Eagle | 0 | -0.0005720 | 4.06e-05 | 1194 | -14.0914190 | 0.0000000 | 21 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000421 | 4.06e-05 | 1194 | 1.0366747 | 0.5538347 | 21 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0006140 | 4.06e-05 | 1194 | 15.1280937 | 0.0000000 | 21 |
| SAS | method | Beagle - Eagle | 0 | -0.0006902 | 4.55e-05 | 1194 | -15.1552930 | 0.0000000 | 21 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0000307 | 4.55e-05 | 1194 | -0.6750046 | 0.7780931 | 21 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0006594 | 4.55e-05 | 1194 | 14.4802884 | 0.0000000 | 21 |
| AFR | method | Beagle - Eagle | 0 | -0.0006710 | 3.48e-05 | 1194 | -19.3021432 | 0.0000000 | 22 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0002068 | 3.48e-05 | 1194 | 5.9504723 | 0.0000000 | 22 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0008778 | 3.48e-05 | 1194 | 25.2526155 | 0.0000000 | 22 |
| AMR | method | Beagle - Eagle | 0 | -0.0006841 | 4.21e-05 | 1194 | -16.2486012 | 0.0000000 | 22 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000762 | 4.21e-05 | 1194 | 1.8101418 | 0.1666555 | 22 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0007604 | 4.21e-05 | 1194 | 18.0587430 | 0.0000000 | 22 |
| EAS | method | Beagle - Eagle | 0 | -0.0009450 | 5.81e-05 | 1194 | -16.2705031 | 0.0000000 | 22 |
| EAS | method | Beagle - SHAPEIT | 0 | 0.0001413 | 5.81e-05 | 1194 | 2.4335804 | 0.0400021 | 22 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0010863 | 5.81e-05 | 1194 | 18.7040835 | 0.0000000 | 22 |
| EUR | method | Beagle - Eagle | 0 | -0.0005896 | 4.76e-05 | 1194 | -12.3746919 | 0.0000000 | 22 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0000589 | 4.76e-05 | 1194 | 1.2353450 | 0.4325231 | 22 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0006484 | 4.76e-05 | 1194 | 13.6100369 | 0.0000000 | 22 |
| SAS | method | Beagle - Eagle | 0 | -0.0007533 | 5.35e-05 | 1194 | -14.0921321 | 0.0000000 | 22 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0001057 | 5.35e-05 | 1194 | 1.9773718 | 0.1182471 | 22 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0008590 | 5.35e-05 | 1194 | 16.0695039 | 0.0000000 | 22 |
| AFR | method | Beagle - Eagle | 0 | -0.0004678 | 1.54e-05 | 1990 | -30.4654146 | 0.0000000 | 23 |
| AFR | method | Beagle - SHAPEIT | 0 | 0.0001173 | 1.54e-05 | 1990 | 7.6403140 | 0.0000000 | 23 |
| AFR | method | Eagle - SHAPEIT | 0 | 0.0005851 | 1.54e-05 | 1990 | 38.1057286 | 0.0000000 | 23 |
| AMR | method | Beagle - Eagle | 0 | -0.0004554 | 1.54e-05 | 1990 | -29.6551906 | 0.0000000 | 23 |
| AMR | method | Beagle - SHAPEIT | 0 | 0.0000767 | 1.54e-05 | 1990 | 4.9958668 | 0.0000019 | 23 |
| AMR | method | Eagle - SHAPEIT | 0 | 0.0005321 | 1.54e-05 | 1990 | 34.6510575 | 0.0000000 | 23 |
| EAS | method | Beagle - Eagle | 0 | -0.0008262 | 1.54e-05 | 1990 | -53.8035422 | 0.0000000 | 23 |
| EAS | method | Beagle - SHAPEIT | 0 | 0.0001816 | 1.54e-05 | 1990 | 11.8266653 | 0.0000000 | 23 |
| EAS | method | Eagle - SHAPEIT | 0 | 0.0010078 | 1.54e-05 | 1990 | 65.6302076 | 0.0000000 | 23 |
| EUR | method | Beagle - Eagle | 0 | -0.0005527 | 1.54e-05 | 1990 | -35.9949554 | 0.0000000 | 23 |
| EUR | method | Beagle - SHAPEIT | 0 | 0.0001158 | 1.54e-05 | 1990 | 7.5391191 | 0.0000000 | 23 |
| EUR | method | Eagle - SHAPEIT | 0 | 0.0006685 | 1.54e-05 | 1990 | 43.5340745 | 0.0000000 | 23 |
| SAS | method | Beagle - Eagle | 0 | -0.0006463 | 1.54e-05 | 1990 | -42.0871894 | 0.0000000 | 23 |
| SAS | method | Beagle - SHAPEIT | 0 | 0.0001813 | 1.54e-05 | 1990 | 11.8061447 | 0.0000000 | 23 |
| SAS | method | Eagle - SHAPEIT | 0 | 0.0008275 | 1.54e-05 | 1990 | 53.8933341 | 0.0000000 | 23 |
df_pop_pop %>% knitr::kable()
| method | term | contrast | null.value | estimate | std.error | df | statistic | adj.p.value | chrom |
|---|---|---|---|---|---|---|---|---|---|
| Beagle | SUPER | AFR - AMR | 0 | -0.0004807 | 0.0000669 | 630.7053 | -7.1848755 | 0.0000000 | 1 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0018942 | 0.0000829 | 630.7053 | -22.8393004 | 0.0000000 | 1 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004813 | 0.0000723 | 630.7053 | -6.6613280 | 0.0000000 | 1 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0013017 | 0.0000781 | 630.7053 | -16.6613976 | 0.0000000 | 1 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0014135 | 0.0000879 | 630.7053 | -16.0817395 | 0.0000000 | 1 |
| Beagle | SUPER | AMR - EUR | 0 | -0.0000007 | 0.0000779 | 630.7053 | -0.0089136 | 1.0000000 | 1 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0008210 | 0.0000834 | 630.7053 | -9.8476033 | 0.0000000 | 1 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0014128 | 0.0000920 | 630.7053 | 15.3496278 | 0.0000000 | 1 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005925 | 0.0000967 | 630.7053 | 6.1260957 | 0.0000000 | 1 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008203 | 0.0000877 | 630.7053 | -9.3501925 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0005460 | 0.0000669 | 630.7053 | -8.1612259 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0023210 | 0.0000829 | 630.7053 | -27.9865987 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0005274 | 0.0000723 | 630.7053 | -7.2992369 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0015324 | 0.0000781 | 630.7053 | -19.6149324 | 0.0000000 | 1 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0017751 | 0.0000879 | 630.7053 | -20.1954142 | 0.0000000 | 1 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000185 | 0.0000779 | 630.7053 | 0.2378093 | 0.9992921 | 1 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0009864 | 0.0000834 | 630.7053 | -11.8318237 | 0.0000000 | 1 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0017936 | 0.0000920 | 630.7053 | 19.4867853 | 0.0000000 | 1 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0007886 | 0.0000967 | 630.7053 | 8.1541414 | 0.0000000 | 1 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010050 | 0.0000877 | 630.7053 | -11.4548630 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005290 | 0.0000669 | 630.7053 | -7.9071873 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0019927 | 0.0000829 | 630.7053 | -24.0280479 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004911 | 0.0000723 | 630.7053 | -6.7960378 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0013509 | 0.0000781 | 630.7053 | -17.2910718 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0014638 | 0.0000879 | 630.7053 | -16.6536301 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0000379 | 0.0000779 | 630.7053 | 0.4864065 | 0.9886045 | 1 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0008219 | 0.0000834 | 630.7053 | -9.8580616 | 0.0000000 | 1 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0015017 | 0.0000920 | 630.7053 | 16.3149894 | 0.0000000 | 1 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0006419 | 0.0000967 | 630.7053 | 6.6368193 | 0.0000000 | 1 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0008598 | 0.0000877 | 630.7053 | -9.7999554 | 0.0000000 | 1 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0005297 | 0.0000643 | 630.6478 | -8.2429775 | 0.0000000 | 2 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0018225 | 0.0000797 | 630.6478 | -22.8765490 | 0.0000000 | 2 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003888 | 0.0000694 | 630.6478 | -5.6016983 | 0.0000003 | 2 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0012416 | 0.0000750 | 630.6478 | -16.5441496 | 0.0000000 | 2 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0012928 | 0.0000844 | 630.6478 | -15.3115428 | 0.0000000 | 2 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001409 | 0.0000748 | 630.6478 | 1.8825834 | 0.3277699 | 2 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0007119 | 0.0000801 | 630.6478 | -8.8887089 | 0.0000000 | 2 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0014337 | 0.0000884 | 630.6478 | 16.2150908 | 0.0000000 | 2 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005809 | 0.0000929 | 630.6478 | 6.2527494 | 0.0000000 | 2 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008528 | 0.0000843 | 630.6478 | -10.1185359 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0005943 | 0.0000643 | 630.6478 | -9.2483756 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0021737 | 0.0000797 | 630.6478 | -27.2843550 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0003927 | 0.0000694 | 630.6478 | -5.6575273 | 0.0000002 | 2 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0014716 | 0.0000750 | 630.6478 | -19.6083904 | 0.0000000 | 2 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0015793 | 0.0000844 | 630.6478 | -18.7053518 | 0.0000000 | 2 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002016 | 0.0000748 | 630.6478 | 2.6941653 | 0.0559223 | 2 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0008772 | 0.0000801 | 630.6478 | -10.9533597 | 0.0000000 | 2 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0017810 | 0.0000884 | 630.6478 | 20.1429117 | 0.0000000 | 2 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0007021 | 0.0000929 | 630.6478 | 7.5572399 | 0.0000000 | 2 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010789 | 0.0000843 | 630.6478 | -12.8012112 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005739 | 0.0000643 | 630.6478 | -8.9302327 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0018882 | 0.0000797 | 630.6478 | -23.7012034 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003934 | 0.0000694 | 630.6478 | -5.6675196 | 0.0000002 | 2 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0012793 | 0.0000750 | 630.6478 | -17.0468442 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0013143 | 0.0000844 | 630.6478 | -15.5665712 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001805 | 0.0000748 | 630.6478 | 2.4116975 | 0.1134719 | 2 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0007054 | 0.0000801 | 630.6478 | -8.8083088 | 0.0000000 | 2 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0014948 | 0.0000884 | 630.6478 | 16.9064698 | 0.0000000 | 2 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0006089 | 0.0000929 | 630.6478 | 6.5538305 | 0.0000000 | 2 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0008859 | 0.0000843 | 630.6478 | -10.5119645 | 0.0000000 | 2 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0004770 | 0.0000612 | 634.3251 | -7.7901000 | 0.0000000 | 3 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0016633 | 0.0000759 | 634.3251 | -21.9124039 | 0.0000000 | 3 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004289 | 0.0000661 | 634.3251 | -6.4854370 | 0.0000000 | 3 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0011775 | 0.0000715 | 634.3251 | -16.4669982 | 0.0000000 | 3 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0011863 | 0.0000804 | 634.3251 | -14.7465064 | 0.0000000 | 3 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000481 | 0.0000713 | 634.3251 | 0.6739613 | 0.9619775 | 3 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0007005 | 0.0000763 | 634.3251 | -9.1798041 | 0.0000000 | 3 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0012344 | 0.0000842 | 634.3251 | 14.6525376 | 0.0000000 | 3 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004858 | 0.0000885 | 634.3251 | 5.4883007 | 0.0000006 | 3 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0007486 | 0.0000803 | 634.3251 | -9.3219533 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0005060 | 0.0000612 | 634.3251 | -8.2636234 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0020504 | 0.0000759 | 634.3251 | -27.0112230 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0004398 | 0.0000661 | 634.3251 | -6.6496732 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0013493 | 0.0000715 | 634.3251 | -18.8703182 | 0.0000000 | 3 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0015444 | 0.0000804 | 634.3251 | -19.1971499 | 0.0000000 | 3 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000662 | 0.0000713 | 634.3251 | 0.9282515 | 0.8859266 | 3 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0008434 | 0.0000763 | 634.3251 | -11.0519090 | 0.0000000 | 3 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0016106 | 0.0000842 | 634.3251 | 19.1178867 | 0.0000000 | 3 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0007010 | 0.0000885 | 634.3251 | 7.9192358 | 0.0000000 | 3 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0009095 | 0.0000803 | 634.3251 | -11.3268008 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005115 | 0.0000612 | 634.3251 | -8.3541310 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0017565 | 0.0000759 | 634.3251 | -23.1393189 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004421 | 0.0000661 | 634.3251 | -6.6851015 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0012366 | 0.0000715 | 634.3251 | -17.2936082 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0012449 | 0.0000804 | 634.3251 | -15.4748812 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0000694 | 0.0000713 | 634.3251 | 0.9731112 | 0.8672733 | 3 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0007251 | 0.0000763 | 634.3251 | -9.5018087 | 0.0000000 | 3 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0013143 | 0.0000842 | 634.3251 | 15.6012950 | 0.0000000 | 3 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0005199 | 0.0000885 | 634.3251 | 5.8726699 | 0.0000001 | 3 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0007945 | 0.0000803 | 634.3251 | -9.8935853 | 0.0000000 | 3 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0005064 | 0.0000560 | 638.4437 | -9.0510630 | 0.0000000 | 4 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0014302 | 0.0000694 | 638.4437 | -20.6181250 | 0.0000000 | 4 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003830 | 0.0000604 | 638.4437 | -6.3378211 | 0.0000000 | 4 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0011164 | 0.0000653 | 638.4437 | -17.0851905 | 0.0000000 | 4 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0009237 | 0.0000735 | 638.4437 | -12.5655292 | 0.0000000 | 4 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001234 | 0.0000652 | 638.4437 | 1.8937125 | 0.3217099 | 4 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0006100 | 0.0000697 | 638.4437 | -8.7472869 | 0.0000000 | 4 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0010471 | 0.0000770 | 638.4437 | 13.6022193 | 0.0000000 | 4 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0003138 | 0.0000809 | 638.4437 | 3.8790612 | 0.0010923 | 4 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0007333 | 0.0000734 | 638.4437 | -9.9940258 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0005953 | 0.0000560 | 638.4437 | -10.6399188 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0018363 | 0.0000694 | 638.4437 | -26.4726774 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0004613 | 0.0000604 | 638.4437 | -7.6331995 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0013117 | 0.0000653 | 638.4437 | -20.0737380 | 0.0000000 | 4 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0012409 | 0.0000735 | 638.4437 | -16.8803516 | 0.0000000 | 4 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0001340 | 0.0000652 | 638.4437 | 2.0565696 | 0.2405037 | 4 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0007163 | 0.0000697 | 638.4437 | -10.2728393 | 0.0000000 | 4 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0013749 | 0.0000770 | 638.4437 | 17.8604780 | 0.0000000 | 4 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0005246 | 0.0000809 | 638.4437 | 6.4853065 | 0.0000000 | 4 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0008503 | 0.0000734 | 638.4437 | -11.5883580 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005658 | 0.0000560 | 638.4437 | -10.1126598 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0015786 | 0.0000694 | 638.4437 | -22.7574952 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004025 | 0.0000604 | 638.4437 | -6.6596682 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0011710 | 0.0000653 | 638.4437 | -17.9210263 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0010127 | 0.0000735 | 638.4437 | -13.7761545 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001633 | 0.0000652 | 638.4437 | 2.5068059 | 0.0903563 | 4 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0006052 | 0.0000697 | 638.4437 | -8.6786878 | 0.0000000 | 4 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0011761 | 0.0000770 | 638.4437 | 15.2772203 | 0.0000000 | 4 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004076 | 0.0000809 | 638.4437 | 5.0384239 | 0.0000061 | 4 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0007685 | 0.0000734 | 638.4437 | -10.4732390 | 0.0000000 | 4 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0004595 | 0.0000644 | 635.1412 | -7.1333934 | 0.0000000 | 5 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0017015 | 0.0000799 | 635.1412 | -21.3077225 | 0.0000000 | 5 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004053 | 0.0000696 | 635.1412 | -5.8257167 | 0.0000001 | 5 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0012484 | 0.0000752 | 635.1412 | -16.5953891 | 0.0000000 | 5 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0012420 | 0.0000846 | 635.1412 | -14.6757849 | 0.0000000 | 5 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000542 | 0.0000750 | 635.1412 | 0.7219579 | 0.9514281 | 5 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0007889 | 0.0000803 | 635.1412 | -9.8270587 | 0.0000000 | 5 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0012962 | 0.0000886 | 635.1412 | 14.6256267 | 0.0000000 | 5 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004531 | 0.0000931 | 635.1412 | 4.8660624 | 0.0000142 | 5 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008430 | 0.0000845 | 635.1412 | -9.9796538 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0004985 | 0.0000644 | 635.1412 | -7.7386505 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0020665 | 0.0000799 | 635.1412 | -25.8787000 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0004383 | 0.0000696 | 635.1412 | -6.2988992 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0014496 | 0.0000752 | 635.1412 | -19.2698312 | 0.0000000 | 5 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0015681 | 0.0000846 | 635.1412 | -18.5281119 | 0.0000000 | 5 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000602 | 0.0000750 | 635.1412 | 0.8028052 | 0.9297348 | 5 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0009511 | 0.0000803 | 635.1412 | -11.8475185 | 0.0000000 | 5 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0016283 | 0.0000886 | 635.1412 | 18.3728150 | 0.0000000 | 5 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0006170 | 0.0000931 | 635.1412 | 6.6253528 | 0.0000000 | 5 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010113 | 0.0000845 | 635.1412 | -11.9714716 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005565 | 0.0000644 | 635.1412 | -8.6396912 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0017921 | 0.0000799 | 635.1412 | -22.4415111 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004322 | 0.0000696 | 635.1412 | -6.2120620 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0013065 | 0.0000752 | 635.1412 | -17.3682064 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0012355 | 0.0000846 | 635.1412 | -14.5991105 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001243 | 0.0000750 | 635.1412 | 1.6571039 | 0.4614777 | 5 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0007500 | 0.0000803 | 635.1412 | -9.3425772 | 0.0000000 | 5 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0013598 | 0.0000886 | 635.1412 | 15.3439122 | 0.0000000 | 5 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004855 | 0.0000931 | 635.1412 | 5.2140274 | 0.0000025 | 5 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0008743 | 0.0000845 | 635.1412 | -10.3496270 | 0.0000000 | 5 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0003974 | 0.0000584 | 639.1428 | -6.8068381 | 0.0000000 | 6 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0014009 | 0.0000724 | 639.1428 | -19.3561855 | 0.0000000 | 6 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003120 | 0.0000631 | 639.1428 | -4.9483428 | 0.0000095 | 6 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0010676 | 0.0000682 | 639.1428 | -15.6596456 | 0.0000000 | 6 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0010035 | 0.0000767 | 639.1428 | -13.0829367 | 0.0000000 | 6 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000853 | 0.0000680 | 639.1428 | 1.2553529 | 0.7186647 | 6 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0006703 | 0.0000728 | 639.1428 | -9.2122375 | 0.0000000 | 6 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0010888 | 0.0000803 | 639.1428 | 13.5560089 | 0.0000000 | 6 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0003332 | 0.0000844 | 639.1428 | 3.9484748 | 0.0008292 | 6 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0007556 | 0.0000766 | 639.1428 | -9.8690271 | 0.0000000 | 6 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0004122 | 0.0000584 | 639.1428 | -7.0599745 | 0.0000000 | 6 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0017487 | 0.0000724 | 639.1428 | -24.1622959 | 0.0000000 | 6 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0002948 | 0.0000631 | 639.1428 | -4.6747109 | 0.0000353 | 6 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0012453 | 0.0000682 | 639.1428 | -18.2656881 | 0.0000000 | 6 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0013366 | 0.0000767 | 639.1428 | -17.4251325 | 0.0000000 | 6 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0001174 | 0.0000680 | 639.1428 | 1.7265394 | 0.4183083 | 6 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0008331 | 0.0000728 | 639.1428 | -11.4511457 | 0.0000000 | 6 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0014539 | 0.0000803 | 639.1428 | 18.1013769 | 0.0000000 | 6 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0005034 | 0.0000844 | 639.1428 | 5.9646487 | 0.0000000 | 6 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0009505 | 0.0000766 | 639.1428 | -12.4150405 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0004373 | 0.0000584 | 639.1428 | -7.4910772 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0014711 | 0.0000724 | 639.1428 | -20.3260321 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003057 | 0.0000631 | 639.1428 | -4.8485485 | 0.0000154 | 6 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0011043 | 0.0000682 | 639.1428 | -16.1971999 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0010337 | 0.0000767 | 639.1428 | -13.4772586 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001316 | 0.0000680 | 639.1428 | 1.9354957 | 0.2995529 | 6 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0006670 | 0.0000728 | 639.1428 | -9.1669233 | 0.0000000 | 6 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0011653 | 0.0000803 | 639.1428 | 14.5082357 | 0.0000000 | 6 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0003668 | 0.0000844 | 639.1428 | 4.3459012 | 0.0001567 | 6 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0007985 | 0.0000766 | 639.1428 | -10.4299050 | 0.0000000 | 6 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0003883 | 0.0000653 | 639.4150 | -5.9473862 | 0.0000000 | 7 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0016532 | 0.0000809 | 639.4150 | -20.4228820 | 0.0000000 | 7 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003161 | 0.0000705 | 639.4150 | -4.4819484 | 0.0000856 | 7 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0011325 | 0.0000763 | 639.4150 | -14.8523711 | 0.0000000 | 7 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0012648 | 0.0000858 | 639.4150 | -14.7435774 | 0.0000000 | 7 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000722 | 0.0000760 | 639.4150 | 0.9499242 | 0.8771082 | 7 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0007442 | 0.0000814 | 639.4150 | -9.1453984 | 0.0000000 | 7 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0013370 | 0.0000898 | 639.4150 | 14.8833148 | 0.0000000 | 7 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005206 | 0.0000944 | 639.4150 | 5.5152983 | 0.0000005 | 7 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008164 | 0.0000856 | 639.4150 | -9.5343018 | 0.0000000 | 7 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0004087 | 0.0000653 | 639.4150 | -6.2599081 | 0.0000000 | 7 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0019425 | 0.0000809 | 639.4150 | -23.9975453 | 0.0000000 | 7 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0003363 | 0.0000705 | 639.4150 | -4.7684742 | 0.0000227 | 7 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0013508 | 0.0000763 | 639.4150 | -17.7147460 | 0.0000000 | 7 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0015338 | 0.0000858 | 639.4150 | -17.8786270 | 0.0000000 | 7 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000724 | 0.0000760 | 639.4150 | 0.9525262 | 0.8760251 | 7 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0009421 | 0.0000814 | 639.4150 | -11.5768551 | 0.0000000 | 7 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0016062 | 0.0000898 | 639.4150 | 17.8793162 | 0.0000000 | 7 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0005917 | 0.0000944 | 639.4150 | 6.2684207 | 0.0000000 | 7 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010145 | 0.0000856 | 639.4150 | -11.8472083 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0004736 | 0.0000653 | 639.4150 | -7.2525270 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0017630 | 0.0000809 | 639.4150 | -21.7805175 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003375 | 0.0000705 | 639.4150 | -4.7859682 | 0.0000208 | 7 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0012010 | 0.0000763 | 639.4150 | -15.7501966 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0012895 | 0.0000858 | 639.4150 | -15.0312212 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001360 | 0.0000760 | 639.4150 | 1.7886923 | 0.3810372 | 7 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0007274 | 0.0000814 | 639.4150 | -8.9394667 | 0.0000000 | 7 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0014255 | 0.0000898 | 639.4150 | 15.8679301 | 0.0000000 | 7 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0005621 | 0.0000944 | 639.4150 | 5.9542350 | 0.0000000 | 7 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0008634 | 0.0000856 | 639.4150 | -10.0833992 | 0.0000000 | 7 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0005456 | 0.0000651 | 643.0653 | -8.3848693 | 0.0000000 | 8 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0017805 | 0.0000807 | 643.0653 | -22.0729241 | 0.0000000 | 8 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004309 | 0.0000703 | 643.0653 | -6.1306601 | 0.0000000 | 8 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0011871 | 0.0000760 | 643.0653 | -15.6221860 | 0.0000000 | 8 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0012349 | 0.0000855 | 643.0653 | -14.4452760 | 0.0000000 | 8 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001147 | 0.0000758 | 643.0653 | 1.5137856 | 0.5538420 | 8 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0006415 | 0.0000811 | 643.0653 | -7.9109164 | 0.0000000 | 8 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0013496 | 0.0000895 | 643.0653 | 15.0757045 | 0.0000000 | 8 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005934 | 0.0000941 | 643.0653 | 6.3083850 | 0.0000000 | 8 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0007562 | 0.0000853 | 643.0653 | -8.8618689 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0006047 | 0.0000651 | 643.0653 | -9.2928435 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0021338 | 0.0000807 | 643.0653 | -26.4523747 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0004708 | 0.0000703 | 643.0653 | -6.6988873 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0013666 | 0.0000760 | 643.0653 | -17.9850130 | 0.0000000 | 8 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0015291 | 0.0000855 | 643.0653 | -17.8864814 | 0.0000000 | 8 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0001338 | 0.0000758 | 643.0653 | 1.7664259 | 0.3942179 | 8 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0007620 | 0.0000811 | 643.0653 | -9.3964716 | 0.0000000 | 8 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0016630 | 0.0000895 | 643.0653 | 18.5756994 | 0.0000000 | 8 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0007671 | 0.0000941 | 643.0653 | 8.1551592 | 0.0000000 | 8 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0008958 | 0.0000853 | 643.0653 | -10.4979159 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0006331 | 0.0000651 | 643.0653 | -9.7302632 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0018328 | 0.0000807 | 643.0653 | -22.7208813 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004444 | 0.0000703 | 643.0653 | -6.3228291 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0012205 | 0.0000760 | 643.0653 | -16.0624092 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0011996 | 0.0000855 | 643.0653 | -14.0326569 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001887 | 0.0000758 | 643.0653 | 2.4908690 | 0.0939318 | 8 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0005874 | 0.0000811 | 643.0653 | -7.2438832 | 0.0000000 | 8 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0013884 | 0.0000895 | 643.0653 | 15.5086769 | 0.0000000 | 8 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0006122 | 0.0000941 | 643.0653 | 6.5084093 | 0.0000000 | 8 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0007762 | 0.0000853 | 643.0653 | -9.0956031 | 0.0000000 | 8 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0003911 | 0.0000759 | 652.0586 | -5.1557551 | 0.0000033 | 9 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0020236 | 0.0000941 | 652.0586 | -21.5162240 | 0.0000000 | 9 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005123 | 0.0000819 | 652.0586 | -6.2518878 | 0.0000000 | 9 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0013780 | 0.0000886 | 652.0586 | -15.5537726 | 0.0000000 | 9 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0016325 | 0.0000997 | 652.0586 | -16.3777400 | 0.0000000 | 9 |
| Beagle | SUPER | AMR - EUR | 0 | -0.0001212 | 0.0000883 | 652.0586 | -1.3716019 | 0.6461377 | 9 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0009869 | 0.0000945 | 652.0586 | -10.4378640 | 0.0000000 | 9 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0015113 | 0.0001044 | 652.0586 | 14.4789160 | 0.0000000 | 9 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0006456 | 0.0001097 | 652.0586 | 5.8862691 | 0.0000001 | 9 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008657 | 0.0000995 | 652.0586 | -8.7011001 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0004335 | 0.0000759 | 652.0586 | -5.7140026 | 0.0000002 | 9 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0025171 | 0.0000941 | 652.0586 | -26.7632832 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0005407 | 0.0000819 | 652.0586 | -6.5984590 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0015570 | 0.0000886 | 652.0586 | -17.5736207 | 0.0000000 | 9 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0020836 | 0.0000997 | 652.0586 | -20.9037721 | 0.0000000 | 9 |
| Eagle | SUPER | AMR - EUR | 0 | -0.0001072 | 0.0000883 | 652.0586 | -1.2136834 | 0.7434499 | 9 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0011235 | 0.0000945 | 652.0586 | -11.8826488 | 0.0000000 | 9 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0019764 | 0.0001044 | 652.0586 | 18.9346882 | 0.0000000 | 9 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0009601 | 0.0001097 | 652.0586 | 8.7540894 | 0.0000000 | 9 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010163 | 0.0000995 | 652.0586 | -10.2142941 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0004942 | 0.0000759 | 652.0586 | -6.5141598 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0021449 | 0.0000941 | 652.0586 | -22.8060605 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0005529 | 0.0000819 | 652.0586 | -6.7469542 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0014366 | 0.0000886 | 652.0586 | -16.2145361 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0016507 | 0.0000997 | 652.0586 | -16.5608711 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AMR - EUR | 0 | -0.0000587 | 0.0000883 | 652.0586 | -0.6643017 | 0.9639017 | 9 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0009424 | 0.0000945 | 652.0586 | -9.9670512 | 0.0000000 | 9 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0015920 | 0.0001044 | 652.0586 | 15.2524531 | 0.0000000 | 9 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0007084 | 0.0001097 | 652.0586 | 6.4585646 | 0.0000000 | 9 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0008837 | 0.0000995 | 652.0586 | -8.8817444 | 0.0000000 | 9 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0004560 | 0.0000632 | 646.0101 | -7.2155670 | 0.0000000 | 10 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0016612 | 0.0000783 | 646.0101 | -21.2058333 | 0.0000000 | 10 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003958 | 0.0000683 | 646.0101 | -5.7992752 | 0.0000001 | 10 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0012602 | 0.0000738 | 646.0101 | -17.0771050 | 0.0000000 | 10 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0012053 | 0.0000830 | 646.0101 | -14.5171021 | 0.0000000 | 10 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000601 | 0.0000736 | 646.0101 | 0.8170491 | 0.9253880 | 10 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0008043 | 0.0000788 | 646.0101 | -10.2125204 | 0.0000000 | 10 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0012654 | 0.0000869 | 646.0101 | 14.5545783 | 0.0000000 | 10 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004010 | 0.0000914 | 646.0101 | 4.3895627 | 0.0001291 | 10 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008644 | 0.0000829 | 646.0101 | -10.4303925 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0004993 | 0.0000632 | 646.0101 | -7.9010580 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0020201 | 0.0000783 | 646.0101 | -25.7866915 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0004126 | 0.0000683 | 646.0101 | -6.0452018 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0015008 | 0.0000738 | 646.0101 | -20.3375258 | 0.0000000 | 10 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0015208 | 0.0000830 | 646.0101 | -18.3176845 | 0.0000000 | 10 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000867 | 0.0000736 | 646.0101 | 1.1775897 | 0.7642543 | 10 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010015 | 0.0000788 | 646.0101 | -12.7176990 | 0.0000000 | 10 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0016075 | 0.0000869 | 646.0101 | 18.4890851 | 0.0000000 | 10 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0005193 | 0.0000914 | 646.0101 | 5.6839751 | 0.0000002 | 10 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010882 | 0.0000829 | 646.0101 | -13.1311916 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005175 | 0.0000632 | 646.0101 | -8.1892208 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0017812 | 0.0000783 | 646.0101 | -22.7372628 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004013 | 0.0000683 | 646.0101 | -5.8789343 | 0.0000001 | 10 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0013267 | 0.0000738 | 646.0101 | -17.9781811 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0012637 | 0.0000830 | 646.0101 | -15.2210328 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001162 | 0.0000736 | 646.0101 | 1.5792674 | 0.5112671 | 10 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0008092 | 0.0000788 | 646.0101 | -10.2756213 | 0.0000000 | 10 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0013799 | 0.0000869 | 646.0101 | 15.8719329 | 0.0000000 | 10 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004545 | 0.0000914 | 646.0101 | 4.9749049 | 0.0000083 | 10 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0009254 | 0.0000829 | 646.0101 | -11.1671763 | 0.0000000 | 10 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0005333 | 0.0000673 | 644.6732 | -7.9205795 | 0.0000000 | 11 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0017392 | 0.0000835 | 644.6732 | -20.8383111 | 0.0000000 | 11 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004278 | 0.0000727 | 644.6732 | -5.8826704 | 0.0000001 | 11 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0012997 | 0.0000786 | 644.6732 | -16.5309460 | 0.0000000 | 11 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0012060 | 0.0000885 | 644.6732 | -13.6337227 | 0.0000000 | 11 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001055 | 0.0000784 | 644.6732 | 1.3451111 | 0.6630158 | 11 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0007665 | 0.0000839 | 644.6732 | -9.1350299 | 0.0000000 | 11 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0013114 | 0.0000926 | 644.6732 | 14.1579502 | 0.0000000 | 11 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004395 | 0.0000973 | 644.6732 | 4.5155908 | 0.0000734 | 11 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008719 | 0.0000883 | 644.6732 | -9.8753590 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0006056 | 0.0000673 | 644.6732 | -8.9955370 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0020909 | 0.0000835 | 644.6732 | -25.0513804 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0004902 | 0.0000727 | 644.6732 | -6.7407832 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0015723 | 0.0000786 | 644.6732 | -19.9973909 | 0.0000000 | 11 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0014852 | 0.0000885 | 644.6732 | -16.7908425 | 0.0000000 | 11 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0001154 | 0.0000784 | 644.6732 | 1.4722585 | 0.5809442 | 11 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0009666 | 0.0000839 | 644.6732 | -11.5207565 | 0.0000000 | 11 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0016007 | 0.0000926 | 644.6732 | 17.2804423 | 0.0000000 | 11 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0005186 | 0.0000973 | 644.6732 | 5.3281924 | 0.0000014 | 11 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010821 | 0.0000883 | 644.6732 | -12.2553998 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005843 | 0.0000673 | 644.6732 | -8.6787111 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0017929 | 0.0000835 | 644.6732 | -21.4809339 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004170 | 0.0000727 | 644.6732 | -5.7337916 | 0.0000002 | 11 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0013256 | 0.0000786 | 644.6732 | -16.8604480 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0012086 | 0.0000885 | 644.6732 | -13.6630476 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001673 | 0.0000784 | 644.6732 | 2.1342368 | 0.2068323 | 11 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0007413 | 0.0000839 | 644.6732 | -8.8354659 | 0.0000000 | 11 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0013759 | 0.0000926 | 644.6732 | 14.8538678 | 0.0000000 | 11 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004672 | 0.0000973 | 644.6732 | 4.8004807 | 0.0000194 | 11 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0009087 | 0.0000883 | 644.6732 | -10.2913976 | 0.0000000 | 11 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0004762 | 0.0000951 | 652.7626 | -5.0094721 | 0.0000070 | 12 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0017950 | 0.0001179 | 652.7626 | -15.2314551 | 0.0000000 | 12 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004501 | 0.0001027 | 652.7626 | -4.3837139 | 0.0001322 | 12 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0014503 | 0.0001110 | 652.7626 | -13.0638189 | 0.0000000 | 12 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0013188 | 0.0001249 | 652.7626 | -10.5590101 | 0.0000000 | 12 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000261 | 0.0001107 | 652.7626 | 0.2356264 | 0.9993175 | 12 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0009741 | 0.0001185 | 652.7626 | -8.2219988 | 0.0000000 | 12 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0013449 | 0.0001308 | 652.7626 | 10.2827046 | 0.0000000 | 12 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0003447 | 0.0001374 | 652.7626 | 2.5083439 | 0.0899880 | 12 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0010002 | 0.0001247 | 652.7626 | -8.0225338 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0005684 | 0.0000951 | 652.7626 | -5.9793994 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0021910 | 0.0001179 | 652.7626 | -18.5913293 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0005112 | 0.0001027 | 652.7626 | -4.9783823 | 0.0000081 | 12 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0016081 | 0.0001110 | 652.7626 | -14.4850317 | 0.0000000 | 12 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0016226 | 0.0001249 | 652.7626 | -12.9910281 | 0.0000000 | 12 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000572 | 0.0001107 | 652.7626 | 0.5169419 | 0.9856670 | 12 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010397 | 0.0001185 | 652.7626 | -8.7754908 | 0.0000000 | 12 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0016798 | 0.0001308 | 652.7626 | 12.8432520 | 0.0000000 | 12 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0005829 | 0.0001374 | 652.7626 | 4.2414451 | 0.0002456 | 12 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010969 | 0.0001247 | 652.7626 | -8.7983103 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005720 | 0.0000951 | 652.7626 | -6.0165577 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0019263 | 0.0001179 | 652.7626 | -16.3450149 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004656 | 0.0001027 | 652.7626 | -4.5341582 | 0.0000673 | 12 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0015731 | 0.0001110 | 652.7626 | -14.1702843 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0013543 | 0.0001249 | 652.7626 | -10.8432093 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001064 | 0.0001107 | 652.7626 | 0.9608960 | 0.8725082 | 12 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0010012 | 0.0001185 | 652.7626 | -8.4507366 | 0.0000000 | 12 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0014607 | 0.0001308 | 652.7626 | 11.1679654 | 0.0000000 | 12 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0003531 | 0.0001374 | 652.7626 | 2.5694430 | 0.0772887 | 12 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0011076 | 0.0001247 | 652.7626 | -8.8839123 | 0.0000000 | 12 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0003963 | 0.0000674 | 660.9148 | -5.8836425 | 0.0000001 | 13 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0018096 | 0.0000835 | 660.9148 | -21.6699623 | 0.0000000 | 13 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004075 | 0.0000728 | 660.9148 | -5.6000461 | 0.0000003 | 13 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0012242 | 0.0000787 | 660.9148 | -15.5626801 | 0.0000000 | 13 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0014133 | 0.0000885 | 660.9148 | -15.9687917 | 0.0000000 | 13 |
| Beagle | SUPER | AMR - EUR | 0 | -0.0000111 | 0.0000784 | 660.9148 | -0.1419189 | 0.9999087 | 13 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0008279 | 0.0000839 | 660.9148 | -9.8621509 | 0.0000000 | 13 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0014021 | 0.0000927 | 660.9148 | 15.1291935 | 0.0000000 | 13 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005854 | 0.0000974 | 660.9148 | 6.0109070 | 0.0000000 | 13 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008168 | 0.0000883 | 660.9148 | -9.2459135 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0005377 | 0.0000674 | 660.9148 | -7.9830149 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0022281 | 0.0000835 | 660.9148 | -26.6819860 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0005174 | 0.0000728 | 660.9148 | -7.1117186 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0015717 | 0.0000787 | 660.9148 | -19.9798086 | 0.0000000 | 13 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0016904 | 0.0000885 | 660.9148 | -19.1000713 | 0.0000000 | 13 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000203 | 0.0000784 | 660.9148 | 0.2587087 | 0.9990134 | 13 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010340 | 0.0000839 | 660.9148 | -12.3167330 | 0.0000000 | 13 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0017107 | 0.0000927 | 660.9148 | 18.4584827 | 0.0000000 | 13 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0006564 | 0.0000974 | 660.9148 | 6.7406680 | 0.0000000 | 13 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010543 | 0.0000883 | 660.9148 | -11.9342267 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0004831 | 0.0000674 | 660.9148 | -7.1713507 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0018470 | 0.0000835 | 660.9148 | -22.1178004 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004246 | 0.0000728 | 660.9148 | -5.8358708 | 0.0000001 | 13 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0013107 | 0.0000787 | 660.9148 | -16.6615922 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0013639 | 0.0000885 | 660.9148 | -15.4112535 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0000584 | 0.0000784 | 660.9148 | 0.7451345 | 0.9457257 | 13 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0008276 | 0.0000839 | 660.9148 | -9.8586381 | 0.0000000 | 13 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0014224 | 0.0000927 | 660.9148 | 15.3475752 | 0.0000000 | 13 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0005363 | 0.0000974 | 660.9148 | 5.5072397 | 0.0000005 | 13 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0008861 | 0.0000883 | 660.9148 | -10.0302434 | 0.0000000 | 13 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0005153 | 0.0000781 | 653.1927 | -6.6005741 | 0.0000000 | 14 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0018119 | 0.0000968 | 653.1927 | -18.7223894 | 0.0000000 | 14 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004380 | 0.0000843 | 653.1927 | -5.1944788 | 0.0000027 | 14 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0013179 | 0.0000912 | 653.1927 | -14.4556755 | 0.0000000 | 14 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0012966 | 0.0001026 | 653.1927 | -12.6419026 | 0.0000000 | 14 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000773 | 0.0000909 | 653.1927 | 0.8499212 | 0.9147422 | 14 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0008026 | 0.0000973 | 653.1927 | -8.2495488 | 0.0000000 | 14 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0013739 | 0.0001074 | 653.1927 | 12.7916893 | 0.0000000 | 14 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004940 | 0.0001129 | 653.1927 | 4.3775452 | 0.0001359 | 14 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008799 | 0.0001024 | 653.1927 | -8.5941837 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0006659 | 0.0000781 | 653.1927 | -8.5299660 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0022729 | 0.0000968 | 653.1927 | -23.4850665 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0004992 | 0.0000843 | 653.1927 | -5.9200570 | 0.0000001 | 14 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0015540 | 0.0000912 | 653.1927 | -17.0458377 | 0.0000000 | 14 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0016070 | 0.0001026 | 653.1927 | -15.6672839 | 0.0000000 | 14 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0001667 | 0.0000909 | 653.1927 | 1.8337321 | 0.3549676 | 14 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0008881 | 0.0000973 | 653.1927 | -9.1285414 | 0.0000000 | 14 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0017737 | 0.0001074 | 653.1927 | 16.5134563 | 0.0000000 | 14 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0007188 | 0.0001129 | 653.1927 | 6.3693024 | 0.0000000 | 14 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010548 | 0.0001024 | 653.1927 | -10.3030689 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0006077 | 0.0000781 | 653.1927 | -7.7846457 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0019249 | 0.0000968 | 653.1927 | -19.8899273 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004454 | 0.0000843 | 653.1927 | -5.2814633 | 0.0000017 | 14 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0013879 | 0.0000912 | 653.1927 | -15.2233350 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0013172 | 0.0001026 | 653.1927 | -12.8423257 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001624 | 0.0000909 | 653.1927 | 1.7860371 | 0.3825800 | 14 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0007802 | 0.0000973 | 653.1927 | -8.0187899 | 0.0000000 | 14 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0014796 | 0.0001074 | 653.1927 | 13.7754085 | 0.0000000 | 14 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0005371 | 0.0001129 | 653.1927 | 4.7586174 | 0.0000236 | 14 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0009425 | 0.0001024 | 653.1927 | -9.2061288 | 0.0000000 | 14 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0004353 | 0.0000914 | 656.1872 | -4.7618899 | 0.0000233 | 15 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0021699 | 0.0001133 | 656.1872 | -19.1473359 | 0.0000000 | 15 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0006028 | 0.0000987 | 656.1872 | -6.1052685 | 0.0000000 | 15 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0015207 | 0.0001068 | 656.1872 | -14.2444128 | 0.0000000 | 15 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0017346 | 0.0001201 | 656.1872 | -14.4423262 | 0.0000000 | 15 |
| Beagle | SUPER | AMR - EUR | 0 | -0.0001675 | 0.0001065 | 656.1872 | -1.5738279 | 0.5147790 | 15 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0010854 | 0.0001139 | 656.1872 | -9.5269507 | 0.0000000 | 15 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0015670 | 0.0001258 | 656.1872 | 12.4595392 | 0.0000000 | 15 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0006492 | 0.0001322 | 656.1872 | 4.9126013 | 0.0000112 | 15 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0009178 | 0.0001199 | 656.1872 | -7.6558970 | 0.0000000 | 15 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0004916 | 0.0000914 | 656.1872 | -5.3780183 | 0.0000010 | 15 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0025493 | 0.0001133 | 656.1872 | -22.4952292 | 0.0000000 | 15 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0005827 | 0.0000987 | 656.1872 | -5.9014491 | 0.0000001 | 15 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0018062 | 0.0001068 | 656.1872 | -16.9190560 | 0.0000000 | 15 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0020577 | 0.0001201 | 656.1872 | -17.1323231 | 0.0000000 | 15 |
| Eagle | SUPER | AMR - EUR | 0 | -0.0000911 | 0.0001065 | 656.1872 | -0.8556841 | 0.9127880 | 15 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0013146 | 0.0001139 | 656.1872 | -11.5388757 | 0.0000000 | 15 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0019666 | 0.0001258 | 656.1872 | 15.6361726 | 0.0000000 | 15 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0007431 | 0.0001322 | 656.1872 | 5.6229133 | 0.0000003 | 15 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0012235 | 0.0001199 | 656.1872 | -10.2054981 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005581 | 0.0000914 | 656.1872 | -6.1051462 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0022967 | 0.0001133 | 656.1872 | -20.2663472 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0006185 | 0.0000987 | 656.1872 | -6.2636999 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0016815 | 0.0001068 | 656.1872 | -15.7515208 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0017386 | 0.0001201 | 656.1872 | -14.4758028 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AMR - EUR | 0 | -0.0000604 | 0.0001065 | 656.1872 | -0.5672865 | 0.9797282 | 15 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0011234 | 0.0001139 | 656.1872 | -9.8613710 | 0.0000000 | 15 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0016782 | 0.0001258 | 656.1872 | 13.3434417 | 0.0000000 | 15 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0006151 | 0.0001322 | 656.1872 | 4.6547380 | 0.0000386 | 15 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0010631 | 0.0001199 | 656.1872 | -8.8674629 | 0.0000000 | 15 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0006495 | 0.0000979 | 653.4378 | -6.6332752 | 0.0000000 | 16 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0023399 | 0.0001214 | 653.4378 | -19.2755192 | 0.0000000 | 16 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005213 | 0.0001058 | 653.4378 | -4.9284923 | 0.0000104 | 16 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0016488 | 0.0001144 | 653.4378 | -14.4187146 | 0.0000000 | 16 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0016904 | 0.0001287 | 653.4378 | -13.1389254 | 0.0000000 | 16 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001283 | 0.0001140 | 653.4378 | 1.1247215 | 0.7934607 | 16 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0009993 | 0.0001220 | 653.4378 | -8.1886747 | 0.0000000 | 16 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0018186 | 0.0001347 | 653.4378 | 13.4989089 | 0.0000000 | 16 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0006911 | 0.0001416 | 653.4378 | 4.8817205 | 0.0000131 | 16 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0011276 | 0.0001284 | 653.4378 | -8.7803472 | 0.0000000 | 16 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0006846 | 0.0000979 | 653.4378 | -6.9910749 | 0.0000000 | 16 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0027536 | 0.0001214 | 653.4378 | -22.6835873 | 0.0000000 | 16 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0006338 | 0.0001058 | 653.4378 | -5.9920944 | 0.0000000 | 16 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0017238 | 0.0001144 | 653.4378 | -15.0738891 | 0.0000000 | 16 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0020691 | 0.0001287 | 653.4378 | -16.0823202 | 0.0000000 | 16 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000508 | 0.0001140 | 653.4378 | 0.4454190 | 0.9918448 | 16 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010392 | 0.0001220 | 653.4378 | -8.5155143 | 0.0000000 | 16 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0021198 | 0.0001347 | 653.4378 | 15.7347283 | 0.0000000 | 16 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0010299 | 0.0001416 | 653.4378 | 7.2749511 | 0.0000000 | 16 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010900 | 0.0001284 | 653.4378 | -8.4877471 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0007895 | 0.0000979 | 653.4378 | -8.0622376 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0025396 | 0.0001214 | 653.4378 | -20.9205306 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0006761 | 0.0001058 | 653.4378 | -6.3923138 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0017614 | 0.0001144 | 653.4378 | -15.4030212 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0017501 | 0.0001287 | 653.4378 | -13.6034830 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001133 | 0.0001140 | 653.4378 | 0.9940318 | 0.8580562 | 16 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0009719 | 0.0001220 | 653.4378 | -7.9644262 | 0.0000000 | 16 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0018635 | 0.0001347 | 653.4378 | 13.8319203 | 0.0000000 | 16 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0007782 | 0.0001416 | 653.4378 | 5.4972279 | 0.0000006 | 16 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0010853 | 0.0001284 | 653.4378 | -8.4511982 | 0.0000000 | 16 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0006515 | 0.0001001 | 650.1826 | -6.5071736 | 0.0000000 | 17 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0026169 | 0.0001241 | 650.1826 | -21.0828180 | 0.0000000 | 17 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0006443 | 0.0001081 | 650.1826 | -5.9577574 | 0.0000000 | 17 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0018114 | 0.0001169 | 650.1826 | -15.4919024 | 0.0000000 | 17 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0019654 | 0.0001315 | 650.1826 | -14.9402023 | 0.0000000 | 17 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000072 | 0.0001166 | 650.1826 | 0.0617274 | 0.9999967 | 17 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0011599 | 0.0001248 | 650.1826 | -9.2955037 | 0.0000000 | 17 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0019726 | 0.0001378 | 650.1826 | 14.3193133 | 0.0000000 | 17 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0008055 | 0.0001447 | 650.1826 | 5.5645944 | 0.0000004 | 17 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0011671 | 0.0001313 | 650.1826 | -8.8882625 | 0.0000000 | 17 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0007019 | 0.0001001 | 650.1826 | -7.0100132 | 0.0000000 | 17 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0029560 | 0.0001241 | 650.1826 | -23.8146589 | 0.0000000 | 17 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0006728 | 0.0001081 | 650.1826 | -6.2209768 | 0.0000000 | 17 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0020983 | 0.0001169 | 650.1826 | -17.9452459 | 0.0000000 | 17 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0022541 | 0.0001315 | 650.1826 | -17.1351420 | 0.0000000 | 17 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000291 | 0.0001166 | 650.1826 | 0.2493794 | 0.9991463 | 17 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0013964 | 0.0001248 | 650.1826 | -11.1909603 | 0.0000000 | 17 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0022832 | 0.0001378 | 650.1826 | 16.5741875 | 0.0000000 | 17 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0008577 | 0.0001447 | 650.1826 | 5.9253957 | 0.0000000 | 17 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0014255 | 0.0001313 | 650.1826 | -10.8561290 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0006865 | 0.0001001 | 650.1826 | -6.8567863 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0027376 | 0.0001241 | 650.1826 | -22.0556858 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0006403 | 0.0001081 | 650.1826 | -5.9202583 | 0.0000001 | 17 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0017637 | 0.0001169 | 650.1826 | -15.0835378 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0020511 | 0.0001315 | 650.1826 | -15.5920660 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0000463 | 0.0001166 | 650.1826 | 0.3967336 | 0.9947687 | 17 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0010771 | 0.0001248 | 650.1826 | -8.6323095 | 0.0000000 | 17 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0020974 | 0.0001378 | 650.1826 | 15.2253554 | 0.0000000 | 17 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0009740 | 0.0001447 | 650.1826 | 6.7287206 | 0.0000000 | 17 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0011234 | 0.0001313 | 650.1826 | -8.5555059 | 0.0000000 | 17 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0005757 | 0.0000783 | 663.0280 | -7.3518272 | 0.0000000 | 18 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0021172 | 0.0000971 | 663.0280 | -21.8100354 | 0.0000000 | 18 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005734 | 0.0000846 | 663.0280 | -6.7792484 | 0.0000000 | 18 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0014635 | 0.0000914 | 663.0280 | -16.0042708 | 0.0000000 | 18 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0015415 | 0.0001029 | 663.0280 | -14.9834938 | 0.0000000 | 18 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000023 | 0.0000912 | 663.0280 | 0.0250746 | 0.9999999 | 18 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0008878 | 0.0000976 | 663.0280 | -9.0978713 | 0.0000000 | 18 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0015438 | 0.0001077 | 663.0280 | 14.3296314 | 0.0000000 | 18 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0006537 | 0.0001132 | 663.0280 | 5.7743071 | 0.0000001 | 18 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0008901 | 0.0001027 | 663.0280 | -8.6679076 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0006346 | 0.0000783 | 663.0280 | -8.1041081 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0025268 | 0.0000971 | 663.0280 | -26.0298431 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0006685 | 0.0000846 | 663.0280 | -7.9039036 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0016961 | 0.0000914 | 663.0280 | -18.5480253 | 0.0000000 | 18 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0018922 | 0.0001029 | 663.0280 | -18.3925675 | 0.0000000 | 18 |
| Eagle | SUPER | AMR - EUR | 0 | -0.0000339 | 0.0000912 | 663.0280 | -0.3721051 | 0.9959161 | 18 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010615 | 0.0000976 | 663.0280 | -10.8778961 | 0.0000000 | 18 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0018583 | 0.0001077 | 663.0280 | 17.2489364 | 0.0000000 | 18 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0008307 | 0.0001132 | 663.0280 | 7.3380322 | 0.0000000 | 18 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010276 | 0.0001027 | 663.0280 | -10.0067727 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0006185 | 0.0000783 | 663.0280 | -7.8983140 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0022082 | 0.0000971 | 663.0280 | -22.7481024 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0006070 | 0.0000846 | 663.0280 | -7.1761223 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0014875 | 0.0000914 | 663.0280 | -16.2661910 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0015898 | 0.0001029 | 663.0280 | -15.4526759 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0000115 | 0.0000912 | 663.0280 | 0.1262350 | 0.9999427 | 18 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0008690 | 0.0000976 | 663.0280 | -8.9048037 | 0.0000000 | 18 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0016013 | 0.0001077 | 663.0280 | 14.8632962 | 0.0000000 | 18 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0007208 | 0.0001132 | 663.0280 | 6.3671379 | 0.0000000 | 18 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0008805 | 0.0001027 | 663.0280 | -8.5742632 | 0.0000000 | 18 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0005653 | 0.0000918 | 666.2443 | -6.1554178 | 0.0000000 | 19 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0024086 | 0.0001139 | 666.2443 | -21.1560070 | 0.0000000 | 19 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005226 | 0.0000992 | 666.2443 | -5.2684408 | 0.0000018 | 19 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0015580 | 0.0001072 | 666.2443 | -14.5267846 | 0.0000000 | 19 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0018433 | 0.0001207 | 666.2443 | -15.2769893 | 0.0000000 | 19 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000427 | 0.0001069 | 666.2443 | 0.3990473 | 0.9946505 | 19 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0009927 | 0.0001145 | 666.2443 | -8.6733780 | 0.0000000 | 19 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0018860 | 0.0001264 | 666.2443 | 14.9264329 | 0.0000000 | 19 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0008506 | 0.0001328 | 666.2443 | 6.4069730 | 0.0000000 | 19 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0010354 | 0.0001204 | 666.2443 | -8.5965874 | 0.0000000 | 19 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0005826 | 0.0000918 | 666.2443 | -6.3439089 | 0.0000000 | 19 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0027000 | 0.0001139 | 666.2443 | -23.7153871 | 0.0000000 | 19 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0005104 | 0.0000992 | 666.2443 | -5.1449956 | 0.0000035 | 19 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0016569 | 0.0001072 | 666.2443 | -15.4490484 | 0.0000000 | 19 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0021174 | 0.0001207 | 666.2443 | -17.5484586 | 0.0000000 | 19 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000722 | 0.0001069 | 666.2443 | 0.6754135 | 0.9616864 | 19 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010743 | 0.0001145 | 666.2443 | -9.3863511 | 0.0000000 | 19 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0021896 | 0.0001264 | 666.2443 | 17.3294761 | 0.0000000 | 19 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0010431 | 0.0001328 | 666.2443 | 7.8566854 | 0.0000000 | 19 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0011465 | 0.0001204 | 666.2443 | -9.5195229 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0006047 | 0.0000918 | 666.2443 | -6.5850303 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0025295 | 0.0001139 | 666.2443 | -22.2178152 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0005555 | 0.0000992 | 666.2443 | -5.6002953 | 0.0000003 | 19 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0016702 | 0.0001072 | 666.2443 | -15.5734930 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0019248 | 0.0001207 | 666.2443 | -15.9518841 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0000492 | 0.0001069 | 666.2443 | 0.4601536 | 0.9907685 | 19 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0010655 | 0.0001145 | 666.2443 | -9.3094866 | 0.0000000 | 19 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0019740 | 0.0001264 | 666.2443 | 15.6226404 | 0.0000000 | 19 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0008593 | 0.0001328 | 666.2443 | 6.4719657 | 0.0000000 | 19 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0011147 | 0.0001204 | 666.2443 | -9.2553370 | 0.0000000 | 19 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0007722 | 0.0001025 | 652.0675 | -7.5365726 | 0.0000000 | 20 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0027695 | 0.0001270 | 652.0675 | -21.8029830 | 0.0000000 | 20 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005905 | 0.0001107 | 652.0675 | -5.3355198 | 0.0000013 | 20 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0017334 | 0.0001197 | 652.0675 | -14.4864655 | 0.0000000 | 20 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0019973 | 0.0001346 | 652.0675 | -14.8362259 | 0.0000000 | 20 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001817 | 0.0001193 | 652.0675 | 1.5228683 | 0.5479119 | 20 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0009612 | 0.0001277 | 652.0675 | -7.5273517 | 0.0000000 | 20 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0021790 | 0.0001410 | 652.0675 | 15.4567275 | 0.0000000 | 20 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0010361 | 0.0001481 | 652.0675 | 6.9943358 | 0.0000000 | 20 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0011429 | 0.0001344 | 652.0675 | -8.5054351 | 0.0000000 | 20 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0008697 | 0.0001025 | 652.0675 | -8.4874557 | 0.0000000 | 20 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0030693 | 0.0001270 | 652.0675 | -24.1633525 | 0.0000000 | 20 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0005752 | 0.0001107 | 652.0675 | -5.1973791 | 0.0000027 | 20 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0019132 | 0.0001197 | 652.0675 | -15.9888272 | 0.0000000 | 20 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0021997 | 0.0001346 | 652.0675 | -16.3396442 | 0.0000000 | 20 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002944 | 0.0001193 | 652.0675 | 2.4675553 | 0.0993608 | 20 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010435 | 0.0001277 | 652.0675 | -8.1721665 | 0.0000000 | 20 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0024941 | 0.0001410 | 652.0675 | 17.6919896 | 0.0000000 | 20 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0011561 | 0.0001481 | 652.0675 | 7.8047927 | 0.0000000 | 20 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0013380 | 0.0001344 | 652.0675 | -9.9570424 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0008548 | 0.0001025 | 652.0675 | -8.3429085 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0028661 | 0.0001270 | 652.0675 | -22.5636566 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0006142 | 0.0001107 | 652.0675 | -5.5490767 | 0.0000004 | 20 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0017982 | 0.0001197 | 652.0675 | -15.0279595 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0020113 | 0.0001346 | 652.0675 | -14.9402499 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0002407 | 0.0001193 | 652.0675 | 2.0172070 | 0.2588100 | 20 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0009434 | 0.0001277 | 652.0675 | -7.3877582 | 0.0000000 | 20 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0022520 | 0.0001410 | 652.0675 | 15.9744717 | 0.0000000 | 20 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0010679 | 0.0001481 | 652.0675 | 7.2092102 | 0.0000000 | 20 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0011841 | 0.0001344 | 652.0675 | -8.8117335 | 0.0000000 | 20 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0002164 | 0.0000976 | 696.3982 | -2.2165641 | 0.1747130 | 21 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0016942 | 0.0001210 | 696.3982 | -13.9967600 | 0.0000000 | 21 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0001822 | 0.0001055 | 696.3982 | -1.7276072 | 0.4175899 | 21 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0011539 | 0.0001140 | 696.3982 | -10.1199434 | 0.0000000 | 21 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0014778 | 0.0001283 | 696.3982 | -11.5197383 | 0.0000000 | 21 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0000342 | 0.0001137 | 696.3982 | 0.3009711 | 0.9982130 | 21 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0009375 | 0.0001217 | 696.3982 | -7.7044437 | 0.0000000 | 21 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0015120 | 0.0001343 | 696.3982 | 11.2554544 | 0.0000000 | 21 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005403 | 0.0001412 | 696.3982 | 3.8276206 | 0.0013258 | 21 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0009717 | 0.0001280 | 696.3982 | -7.5887283 | 0.0000000 | 21 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0002526 | 0.0000976 | 696.3982 | -2.5873233 | 0.0737863 | 21 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0020187 | 0.0001210 | 696.3982 | -16.6779455 | 0.0000000 | 21 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0002613 | 0.0001055 | 696.3982 | -2.4777356 | 0.0968707 | 21 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0013512 | 0.0001140 | 696.3982 | -11.8505178 | 0.0000000 | 21 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0017661 | 0.0001283 | 696.3982 | -13.7674105 | 0.0000000 | 21 |
| Eagle | SUPER | AMR - EUR | 0 | -0.0000087 | 0.0001137 | 696.3982 | -0.0764366 | 0.9999923 | 21 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010986 | 0.0001217 | 696.3982 | -9.0286020 | 0.0000000 | 21 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0017574 | 0.0001343 | 696.3982 | 13.0824203 | 0.0000000 | 21 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0006675 | 0.0001412 | 696.3982 | 4.7288336 | 0.0000269 | 21 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0010899 | 0.0001280 | 696.3982 | -8.5119437 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0003551 | 0.0000976 | 696.3982 | -3.6365712 | 0.0027379 | 21 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0017594 | 0.0001210 | 696.3982 | -14.5360105 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0002181 | 0.0001055 | 696.3982 | -2.0678150 | 0.2353156 | 21 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0012626 | 0.0001140 | 696.3982 | -11.0732426 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0014044 | 0.0001283 | 696.3982 | -10.9477579 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0001370 | 0.0001137 | 696.3982 | 1.2048120 | 0.7486242 | 21 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0009075 | 0.0001217 | 696.3982 | -7.4583250 | 0.0000000 | 21 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0015414 | 0.0001343 | 696.3982 | 11.4742535 | 0.0000000 | 21 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004969 | 0.0001412 | 696.3982 | 3.5199665 | 0.0041855 | 21 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0010445 | 0.0001280 | 696.3982 | -8.1574183 | 0.0000000 | 21 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0004068 | 0.0001265 | 677.1751 | -3.2154756 | 0.0118738 | 22 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0025320 | 0.0001568 | 677.1751 | -16.1443411 | 0.0000000 | 22 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005019 | 0.0001366 | 677.1751 | -3.6726859 | 0.0023985 | 22 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0016743 | 0.0001477 | 677.1751 | -11.3328909 | 0.0000000 | 22 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0021252 | 0.0001662 | 677.1751 | -12.7858221 | 0.0000000 | 22 |
| Beagle | SUPER | AMR - EUR | 0 | -0.0000951 | 0.0001473 | 677.1751 | -0.6454124 | 0.9674745 | 22 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0012675 | 0.0001577 | 677.1751 | -8.0395209 | 0.0000000 | 22 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0020301 | 0.0001741 | 677.1751 | 11.6634779 | 0.0000000 | 22 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0008577 | 0.0001829 | 677.1751 | 4.6893952 | 0.0000326 | 22 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0011724 | 0.0001659 | 677.1751 | -7.0667990 | 0.0000000 | 22 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0004200 | 0.0001265 | 677.1751 | -3.3196563 | 0.0084076 | 22 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0028060 | 0.0001568 | 677.1751 | -17.8915712 | 0.0000000 | 22 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0004205 | 0.0001366 | 677.1751 | -3.0770329 | 0.0184482 | 22 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0017566 | 0.0001477 | 677.1751 | -11.8900892 | 0.0000000 | 22 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0023860 | 0.0001662 | 677.1751 | -14.3551479 | 0.0000000 | 22 |
| Eagle | SUPER | AMR - EUR | 0 | -0.0000005 | 0.0001473 | 677.1751 | -0.0034443 | 1.0000000 | 22 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0013367 | 0.0001577 | 677.1751 | -8.4780557 | 0.0000000 | 22 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0023855 | 0.0001741 | 677.1751 | 13.7054575 | 0.0000000 | 22 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0010494 | 0.0001829 | 677.1751 | 5.7375731 | 0.0000001 | 22 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0013362 | 0.0001659 | 677.1751 | -8.0535776 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005374 | 0.0001265 | 677.1751 | -4.2480443 | 0.0002377 | 22 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0025975 | 0.0001568 | 677.1751 | -16.5620008 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0006499 | 0.0001366 | 677.1751 | -4.7556728 | 0.0000238 | 22 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0017755 | 0.0001477 | 677.1751 | -12.0175142 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0020601 | 0.0001662 | 677.1751 | -12.3940007 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AMR - EUR | 0 | -0.0001124 | 0.0001473 | 677.1751 | -0.7632502 | 0.9409835 | 22 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0012380 | 0.0001577 | 677.1751 | -7.8525184 | 0.0000000 | 22 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0019476 | 0.0001741 | 677.1751 | 11.1895725 | 0.0000000 | 22 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0008220 | 0.0001829 | 677.1751 | 4.4945101 | 0.0000801 | 22 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0011256 | 0.0001659 | 677.1751 | -6.7844566 | 0.0000000 | 22 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0003326 | 0.0000593 | 1089.0700 | -5.6083028 | 0.0000003 | 23 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0019472 | 0.0000593 | 1089.0700 | -32.8312056 | 0.0000000 | 23 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0006228 | 0.0000593 | 1089.0700 | -10.5014284 | 0.0000000 | 23 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0011571 | 0.0000593 | 1089.0700 | -19.5101249 | 0.0000000 | 23 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0016146 | 0.0000593 | 1089.0700 | -27.2229028 | 0.0000000 | 23 |
| Beagle | SUPER | AMR - EUR | 0 | -0.0002902 | 0.0000593 | 1089.0700 | -4.8931256 | 0.0000113 | 23 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0008245 | 0.0000593 | 1089.0700 | -13.9018222 | 0.0000000 | 23 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0013244 | 0.0000593 | 1089.0700 | 22.3297772 | 0.0000000 | 23 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0007901 | 0.0000593 | 1089.0700 | 13.3210806 | 0.0000000 | 23 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0005343 | 0.0000593 | 1089.0700 | -9.0086966 | 0.0000000 | 23 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0003202 | 0.0000593 | 1089.0700 | -5.3985365 | 0.0000008 | 23 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0023056 | 0.0000593 | 1089.0700 | -38.8734268 | 0.0000000 | 23 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0007077 | 0.0000593 | 1089.0700 | -11.9330217 | 0.0000000 | 23 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0013356 | 0.0000593 | 1089.0700 | -22.5189925 | 0.0000000 | 23 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0019854 | 0.0000593 | 1089.0700 | -33.4748903 | 0.0000000 | 23 |
| Eagle | SUPER | AMR - EUR | 0 | -0.0003876 | 0.0000593 | 1089.0700 | -6.5344852 | 0.0000000 | 23 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010154 | 0.0000593 | 1089.0700 | -17.1204559 | 0.0000000 | 23 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0015978 | 0.0000593 | 1089.0700 | 26.9404051 | 0.0000000 | 23 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0009700 | 0.0000593 | 1089.0700 | 16.3544343 | 0.0000000 | 23 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0006278 | 0.0000593 | 1089.0700 | -10.5859707 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0003732 | 0.0000593 | 1089.0700 | -6.2929479 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0018829 | 0.0000593 | 1089.0700 | -31.7473628 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0006244 | 0.0000593 | 1089.0700 | -10.5276276 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0010932 | 0.0000593 | 1089.0700 | -18.4315950 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0015097 | 0.0000593 | 1089.0700 | -25.4544149 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AMR - EUR | 0 | -0.0002512 | 0.0000593 | 1089.0700 | -4.2346797 | 0.0002401 | 23 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0007199 | 0.0000593 | 1089.0700 | -12.1386471 | 0.0000000 | 23 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0012585 | 0.0000593 | 1089.0700 | 21.2197352 | 0.0000000 | 23 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0007898 | 0.0000593 | 1089.0700 | 13.3157679 | 0.0000000 | 23 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0004688 | 0.0000593 | 1089.0700 | -7.9039673 | 0.0000000 | 23 |
# df_flips <- df_switch_trio[[1]] %>%
# mutate(Eagle = (n_flip_eagle) / n_hets,
# Beagle = (n_flip_beagle) / n_hets,
# SHAPEIT = (n_flip_shapeit) / n_hets) %>%
# select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
# mutate(chrom = 1)
#
# for(i in 2:22){
# df_flips <- bind_rows(df_flips,
# {
# df_switch_trio[[i]] %>%
# mutate(Eagle = (n_flip_eagle) / n_hets,
# Beagle = (n_flip_beagle) / n_hets,
# SHAPEIT = (n_flip_shapeit) / n_hets) %>%
# select(Eagle, Beagle, SHAPEIT, SUPER, pair_id) %>%
# mutate(chrom = i)
# })
# }
df_flips <- df_switch_trio_noth %>%
mutate(Eagle = (n_flip_e) / n_het,
Beagle = (n_flip_b) / n_het,
SHAPEIT = (n_flip_s) / n_het) %>%
select(Eagle, Beagle, SHAPEIT, sample, chrom)
df_flips <- df_flips %>%
left_join({df_subj_rel %>% select(id2, SUPER)}, by = c("sample" = "id2")) %>%
rename(pair_id = sample) %>%
select(Eagle, Beagle, SHAPEIT, SUPER, pair_id, chrom)
df_flips <- df_flips %>%
bind_rows({df_switch_x %>%
mutate(Eagle = (n_flip_eagle) / n_hets,
Beagle = (n_flip_beagle) / n_hets,
SHAPEIT = (n_flip_shapeit) / n_hets) %>%
rename(SUPER = pop) %>%
select(Eagle, Beagle, SHAPEIT, SUPER) %>%
mutate(pair_id = 603:1602, chrom = 23)})
df_flips %>%
group_by(chrom) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
knitr::kable()
| chrom | Beagle | Eagle | SHAPEIT |
|---|---|---|---|
| 1 | 0.0057436 | 0.0049992 | 0.0062407 |
| 2 | 0.0058785 | 0.0050772 | 0.0064003 |
| 3 | 0.0055282 | 0.0047878 | 0.0060123 |
| 4 | 0.0052003 | 0.0045228 | 0.0056534 |
| 5 | 0.0055357 | 0.0048034 | 0.0060346 |
| 6 | 0.0050140 | 0.0043553 | 0.0054361 |
| 7 | 0.0055456 | 0.0048417 | 0.0060457 |
| 8 | 0.0055975 | 0.0048655 | 0.0061065 |
| 9 | 0.0061151 | 0.0053432 | 0.0066371 |
| 10 | 0.0054473 | 0.0047538 | 0.0059287 |
| 11 | 0.0055329 | 0.0048044 | 0.0060011 |
| 12 | 0.0055251 | 0.0047841 | 0.0060263 |
| 13 | 0.0052888 | 0.0045885 | 0.0057716 |
| 14 | 0.0057178 | 0.0050183 | 0.0062432 |
| 15 | 0.0061150 | 0.0053937 | 0.0066694 |
| 16 | 0.0064066 | 0.0055367 | 0.0069591 |
| 17 | 0.0063643 | 0.0056145 | 0.0069171 |
| 18 | 0.0055085 | 0.0047830 | 0.0060110 |
| 19 | 0.0059452 | 0.0051986 | 0.0064004 |
| 20 | 0.0060847 | 0.0053683 | 0.0065812 |
| 21 | 0.0060175 | 0.0054222 | 0.0065460 |
| 22 | 0.0066474 | 0.0060262 | 0.0071902 |
| 23 | 0.0013794 | 0.0013749 | 0.0015596 |
df_flips %>%
group_by(chrom, SUPER) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
knitr::kable()
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.
| chrom | SUPER | Beagle | Eagle | SHAPEIT |
|---|---|---|---|---|
| 1 | AFR | 0.0048509 | 0.0038606 | 0.0052944 |
| 1 | AMR | 0.0055828 | 0.0049953 | 0.0061469 |
| 1 | EAS | 0.0074943 | 0.0068074 | 0.0080115 |
| 1 | EUR | 0.0054117 | 0.0049288 | 0.0057730 |
| 1 | SAS | 0.0070490 | 0.0062545 | 0.0077186 |
| 2 | AFR | 0.0049356 | 0.0039058 | 0.0054038 |
| 2 | AMR | 0.0058569 | 0.0051911 | 0.0063823 |
| 2 | EAS | 0.0076922 | 0.0070001 | 0.0083523 |
| 2 | EUR | 0.0053915 | 0.0048466 | 0.0058080 |
| 2 | SAS | 0.0072199 | 0.0063251 | 0.0078776 |
| 3 | AFR | 0.0046336 | 0.0036385 | 0.0050852 |
| 3 | AMR | 0.0054302 | 0.0048384 | 0.0059500 |
| 3 | EAS | 0.0072600 | 0.0065980 | 0.0077701 |
| 3 | EUR | 0.0052122 | 0.0047396 | 0.0055768 |
| 3 | SAS | 0.0067326 | 0.0059511 | 0.0073641 |
| 4 | AFR | 0.0043179 | 0.0034037 | 0.0047116 |
| 4 | AMR | 0.0052432 | 0.0047134 | 0.0057537 |
| 4 | EAS | 0.0066767 | 0.0061394 | 0.0072441 |
| 4 | EUR | 0.0048553 | 0.0043933 | 0.0052107 |
| 4 | SAS | 0.0064016 | 0.0056557 | 0.0069288 |
| 5 | AFR | 0.0046907 | 0.0036968 | 0.0051276 |
| 5 | AMR | 0.0053647 | 0.0048383 | 0.0059255 |
| 5 | EAS | 0.0071985 | 0.0065383 | 0.0078239 |
| 5 | EUR | 0.0051649 | 0.0046727 | 0.0055210 |
| 5 | SAS | 0.0068679 | 0.0060593 | 0.0074859 |
| 6 | AFR | 0.0042879 | 0.0034016 | 0.0046848 |
| 6 | AMR | 0.0049184 | 0.0044419 | 0.0053747 |
| 6 | EAS | 0.0065134 | 0.0059035 | 0.0069773 |
| 6 | EUR | 0.0045903 | 0.0041417 | 0.0048986 |
| 6 | SAS | 0.0061483 | 0.0054287 | 0.0066827 |
| 7 | AFR | 0.0047125 | 0.0038187 | 0.0052157 |
| 7 | AMR | 0.0054486 | 0.0048671 | 0.0059390 |
| 7 | EAS | 0.0072970 | 0.0066100 | 0.0078103 |
| 7 | EUR | 0.0050546 | 0.0046022 | 0.0054386 |
| 7 | SAS | 0.0068066 | 0.0060233 | 0.0074503 |
| 8 | AFR | 0.0046627 | 0.0036525 | 0.0051578 |
| 8 | AMR | 0.0055686 | 0.0050487 | 0.0061625 |
| 8 | EAS | 0.0074901 | 0.0067916 | 0.0079265 |
| 8 | EUR | 0.0051737 | 0.0046984 | 0.0055363 |
| 8 | SAS | 0.0067852 | 0.0060173 | 0.0074357 |
| 9 | AFR | 0.0053080 | 0.0042986 | 0.0058223 |
| 9 | AMR | 0.0058838 | 0.0052889 | 0.0064634 |
| 9 | EAS | 0.0079478 | 0.0072104 | 0.0084824 |
| 9 | EUR | 0.0057032 | 0.0051775 | 0.0060412 |
| 9 | SAS | 0.0073625 | 0.0065280 | 0.0080306 |
| 10 | AFR | 0.0047047 | 0.0037686 | 0.0051588 |
| 10 | AMR | 0.0053361 | 0.0047940 | 0.0058426 |
| 10 | EAS | 0.0069913 | 0.0063791 | 0.0075465 |
| 10 | EUR | 0.0050001 | 0.0045181 | 0.0053389 |
| 10 | SAS | 0.0066376 | 0.0059388 | 0.0072602 |
| 11 | AFR | 0.0046181 | 0.0036593 | 0.0050623 |
| 11 | AMR | 0.0055062 | 0.0049217 | 0.0059881 |
| 11 | EAS | 0.0071875 | 0.0065083 | 0.0077529 |
| 11 | EUR | 0.0050552 | 0.0045970 | 0.0054001 |
| 11 | SAS | 0.0069390 | 0.0061409 | 0.0075149 |
| 12 | AFR | 0.0046534 | 0.0036729 | 0.0051003 |
| 12 | AMR | 0.0054161 | 0.0048634 | 0.0059321 |
| 12 | EAS | 0.0071733 | 0.0065287 | 0.0077276 |
| 12 | EUR | 0.0050806 | 0.0045860 | 0.0054733 |
| 12 | SAS | 0.0069257 | 0.0060555 | 0.0076233 |
| 13 | AFR | 0.0045223 | 0.0035729 | 0.0049646 |
| 13 | AMR | 0.0051376 | 0.0045220 | 0.0056553 |
| 13 | EAS | 0.0068749 | 0.0062732 | 0.0073886 |
| 13 | EUR | 0.0049592 | 0.0044487 | 0.0052886 |
| 13 | SAS | 0.0064168 | 0.0058462 | 0.0071055 |
| 14 | AFR | 0.0048613 | 0.0039247 | 0.0053367 |
| 14 | AMR | 0.0058033 | 0.0051849 | 0.0063353 |
| 14 | EAS | 0.0072085 | 0.0066774 | 0.0078172 |
| 14 | EUR | 0.0052080 | 0.0047903 | 0.0056560 |
| 14 | SAS | 0.0069843 | 0.0062172 | 0.0076441 |
| 15 | AFR | 0.0052719 | 0.0043389 | 0.0057695 |
| 15 | AMR | 0.0058980 | 0.0052902 | 0.0064864 |
| 15 | EAS | 0.0078680 | 0.0071805 | 0.0084877 |
| 15 | EUR | 0.0057784 | 0.0052837 | 0.0061797 |
| 15 | SAS | 0.0073972 | 0.0066798 | 0.0081686 |
| 16 | AFR | 0.0054590 | 0.0044255 | 0.0059674 |
| 16 | AMR | 0.0062847 | 0.0055285 | 0.0068819 |
| 16 | EAS | 0.0083862 | 0.0075083 | 0.0089120 |
| 16 | EUR | 0.0058224 | 0.0053356 | 0.0063845 |
| 16 | SAS | 0.0079026 | 0.0067608 | 0.0084978 |
| 17 | AFR | 0.0053959 | 0.0044922 | 0.0059663 |
| 17 | AMR | 0.0061923 | 0.0055368 | 0.0067498 |
| 17 | EAS | 0.0084273 | 0.0076490 | 0.0089135 |
| 17 | EUR | 0.0058933 | 0.0053589 | 0.0063126 |
| 17 | SAS | 0.0077768 | 0.0069920 | 0.0085050 |
| 18 | AFR | 0.0045757 | 0.0036446 | 0.0050768 |
| 18 | AMR | 0.0055084 | 0.0048932 | 0.0060666 |
| 18 | EAS | 0.0072546 | 0.0065974 | 0.0077358 |
| 18 | EUR | 0.0051053 | 0.0046441 | 0.0054570 |
| 18 | SAS | 0.0067430 | 0.0059354 | 0.0073668 |
| 19 | AFR | 0.0050913 | 0.0041413 | 0.0055110 |
| 19 | AMR | 0.0058473 | 0.0052828 | 0.0063396 |
| 19 | EAS | 0.0077344 | 0.0069670 | 0.0082385 |
| 19 | EUR | 0.0055367 | 0.0050112 | 0.0058588 |
| 19 | SAS | 0.0071206 | 0.0063006 | 0.0077262 |
| 20 | AFR | 0.0050893 | 0.0041390 | 0.0055168 |
| 20 | AMR | 0.0060918 | 0.0054615 | 0.0066459 |
| 20 | EAS | 0.0080383 | 0.0074367 | 0.0086405 |
| 20 | EUR | 0.0055472 | 0.0051462 | 0.0059501 |
| 20 | SAS | 0.0074489 | 0.0066526 | 0.0080439 |
| 21 | AFR | 0.0053831 | 0.0045895 | 0.0059090 |
| 21 | AMR | 0.0059039 | 0.0054901 | 0.0064466 |
| 21 | EAS | 0.0073858 | 0.0067774 | 0.0078760 |
| 21 | EUR | 0.0055923 | 0.0051591 | 0.0060380 |
| 21 | SAS | 0.0070768 | 0.0064655 | 0.0077258 |
| 22 | AFR | 0.0059118 | 0.0050632 | 0.0064401 |
| 22 | AMR | 0.0065342 | 0.0060244 | 0.0070762 |
| 22 | EAS | 0.0082989 | 0.0077582 | 0.0088412 |
| 22 | EUR | 0.0060571 | 0.0056668 | 0.0064708 |
| 22 | SAS | 0.0079135 | 0.0072917 | 0.0086547 |
| 23 | AFR | 0.0010081 | 0.0009991 | 0.0011945 |
| 23 | AMR | 0.0011009 | 0.0010802 | 0.0012704 |
| 23 | EAS | 0.0019555 | 0.0019427 | 0.0021114 |
| 23 | EUR | 0.0012423 | 0.0012304 | 0.0014230 |
| 23 | SAS | 0.0015903 | 0.0016220 | 0.0017988 |
df_flips %>%
group_by(chrom) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
ggplot(aes(x = chrom, y = error_rate, colour = method, shape = method)) +
geom_point(size=3) +
theme_bw() +
xlab("Chromosome") +
ylab("Flip Rate") +
labs(colour = "Method", shape = "Method") +
scale_colour_brewer(palette = "Set2") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
scale_x_continuous("Chromosome", labels = as.character(unique(df_flips$chrom)), breaks = unique(df_flips$chrom))

df_flips %>%
group_by(chrom, SUPER) %>%
summarise(Beagle = mean(Beagle),
Eagle = mean(Eagle),
SHAPEIT = mean(SHAPEIT)) %>%
pivot_longer(Beagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
ggplot(aes(x = chrom, y = error_rate, colour = SUPER, shape = method)) +
geom_point(size=2) +
theme_bw() +
ylab("Flip Rate") +
xlab("Chromosome") +
labs(colour = "Population", shape = "Method") +
scale_colour_brewer(palette = "Set1") +
theme(axis.text.x = element_text(angle = 90, vjust = 0.5)) +
scale_x_continuous("Chromosome", labels = as.character(unique(df_flips$chrom)), breaks = unique(df_flips$chrom))
`summarise()` has grouped output by 'chrom'. You can override using the
`.groups` argument.

# Beagle
autosomes <- df_flips %>% filter(chrom < 23) %>% pull(Beagle)
chrX <- df_flips %>% filter(chrom == 23) %>% pull(Beagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 0.00438 0.00576 0.00138 207. 0 2957. 0.00434 0.00442
# ℹ 2 more variables: method <chr>, alternative <chr>
# Eagle
autosomes <- df_flips %>% filter(chrom < 23) %>% pull(Eagle)
chrX <- df_flips %>% filter(chrom == 23) %>% pull(Eagle)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 0.00367 0.00504 0.00137 176. 0 3336. 0.00362 0.00371
# ℹ 2 more variables: method <chr>, alternative <chr>
# SHAPEIT
autosomes <- df_flips %>% filter(chrom < 23) %>% pull(SHAPEIT)
chrX <- df_flips %>% filter(chrom == 23) %>% pull(SHAPEIT)
t.test(autosomes, chrX) %>% broom::tidy()
# A tibble: 1 × 10
estimate estimate1 estimate2 statistic p.value parameter conf.low conf.high
<dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl> <dbl>
1 0.00470 0.00626 0.00156 217. 0 2802. 0.00466 0.00475
# ℹ 2 more variables: method <chr>, alternative <chr>
mod_fit <- df_flips %>%
filter(chrom == 1) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
df_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)
df_pairwise <- emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
for(i in 2:23){
mod_fit <- df_flips %>%
filter(chrom == i) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method + (1|pair_id), data = .)}
df_anova <- df_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
df_pairwise <- df_pairwise %>% bind_rows({
emmeans::emmeans(mod_fit, ~ method) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
}
df_anova %>%
knitr::kable()
| term | sumsq | meansq | NumDF | DenDF | statistic | p.value | chrom |
|---|---|---|---|---|---|---|---|
| method | 0.0004701 | 0.0002351 | 2 | 1202 | 3013.4749 | 0 | 1 |
| method | 0.0005348 | 0.0002674 | 2 | 1202 | 3318.1790 | 0 | 2 |
| method | 0.0004579 | 0.0002290 | 2 | 1202 | 3011.9306 | 0 | 3 |
| method | 0.0003898 | 0.0001949 | 2 | 1202 | 2569.4671 | 0 | 4 |
| method | 0.0004617 | 0.0002308 | 2 | 1202 | 2718.1027 | 0 | 5 |
| method | 0.0003572 | 0.0001786 | 2 | 1202 | 2679.0043 | 0 | 6 |
| method | 0.0004406 | 0.0002203 | 2 | 1202 | 2572.5825 | 0 | 7 |
| method | 0.0004686 | 0.0002343 | 2 | 1202 | 2046.3998 | 0 | 8 |
| method | 0.0005101 | 0.0002551 | 2 | 1202 | 2506.4370 | 0 | 9 |
| method | 0.0004200 | 0.0002100 | 2 | 1202 | 2375.3062 | 0 | 10 |
| method | 0.0004379 | 0.0002189 | 2 | 1202 | 2188.9479 | 0 | 11 |
| method | 0.0004703 | 0.0002351 | 2 | 1202 | 2259.7295 | 0 | 12 |
| method | 0.0004261 | 0.0002130 | 2 | 1202 | 1679.8712 | 0 | 13 |
| method | 0.0004547 | 0.0002273 | 2 | 1202 | 1921.3314 | 0 | 14 |
| method | 0.0004926 | 0.0002463 | 2 | 1202 | 1943.4193 | 0 | 15 |
| method | 0.0006191 | 0.0003095 | 2 | 1202 | 1781.7578 | 0 | 16 |
| method | 0.0005146 | 0.0002573 | 2 | 1202 | 1661.9270 | 0 | 17 |
| method | 0.0004589 | 0.0002294 | 2 | 1202 | 1880.3071 | 0 | 18 |
| method | 0.0004433 | 0.0002216 | 2 | 1202 | 1421.4820 | 0 | 19 |
| method | 0.0004476 | 0.0002238 | 2 | 1202 | 1429.7051 | 0 | 20 |
| method | 0.0003806 | 0.0001903 | 2 | 1202 | 991.8020 | 0 | 21 |
| method | 0.0004084 | 0.0002042 | 2 | 1202 | 887.5711 | 0 | 22 |
| method | 0.0000222 | 0.0000111 | 2 | 1998 | 638.9949 | 0 | 23 |
df_pairwise %>%
knitr::kable()
| term | contrast | null.value | estimate | std.error | df | statistic | adj.p.value | chrom |
|---|---|---|---|---|---|---|---|---|
| method | Beagle - Eagle | 0 | 0.0007445 | 1.61e-05 | 1202 | 46.2469554 | 0.0000000 | 1 |
| method | Beagle - SHAPEIT | 0 | -0.0004971 | 1.61e-05 | 1202 | -30.8776948 | 0.0000000 | 1 |
| method | Eagle - SHAPEIT | 0 | -0.0012416 | 1.61e-05 | 1202 | -77.1246502 | 0.0000000 | 1 |
| method | Beagle - Eagle | 0 | 0.0008013 | 1.64e-05 | 1202 | 48.9749823 | 0.0000000 | 2 |
| method | Beagle - SHAPEIT | 0 | -0.0005218 | 1.64e-05 | 1202 | -31.8894262 | 0.0000000 | 2 |
| method | Eagle - SHAPEIT | 0 | -0.0013231 | 1.64e-05 | 1202 | -80.8644085 | 0.0000000 | 2 |
| method | Beagle - Eagle | 0 | 0.0007405 | 1.59e-05 | 1202 | 46.5936902 | 0.0000000 | 3 |
| method | Beagle - SHAPEIT | 0 | -0.0004840 | 1.59e-05 | 1202 | -30.4587775 | 0.0000000 | 3 |
| method | Eagle - SHAPEIT | 0 | -0.0012245 | 1.59e-05 | 1202 | -77.0524677 | 0.0000000 | 3 |
| method | Beagle - Eagle | 0 | 0.0006775 | 1.59e-05 | 1202 | 42.6785421 | 0.0000000 | 4 |
| method | Beagle - SHAPEIT | 0 | -0.0004531 | 1.59e-05 | 1202 | -28.5416595 | 0.0000000 | 4 |
| method | Eagle - SHAPEIT | 0 | -0.0011306 | 1.59e-05 | 1202 | -71.2202016 | 0.0000000 | 4 |
| method | Beagle - Eagle | 0 | 0.0007323 | 1.68e-05 | 1202 | 43.5946151 | 0.0000000 | 5 |
| method | Beagle - SHAPEIT | 0 | -0.0004988 | 1.68e-05 | 1202 | -29.6981900 | 0.0000000 | 5 |
| method | Eagle - SHAPEIT | 0 | -0.0012311 | 1.68e-05 | 1202 | -73.2928051 | 0.0000000 | 5 |
| method | Beagle - Eagle | 0 | 0.0006586 | 1.49e-05 | 1202 | 44.2577383 | 0.0000000 | 6 |
| method | Beagle - SHAPEIT | 0 | -0.0004221 | 1.49e-05 | 1202 | -28.3631688 | 0.0000000 | 6 |
| method | Eagle - SHAPEIT | 0 | -0.0010807 | 1.49e-05 | 1202 | -72.6209071 | 0.0000000 | 6 |
| method | Beagle - Eagle | 0 | 0.0007039 | 1.69e-05 | 1202 | 41.7366488 | 0.0000000 | 7 |
| method | Beagle - SHAPEIT | 0 | -0.0005001 | 1.69e-05 | 1202 | -29.6530856 | 0.0000000 | 7 |
| method | Eagle - SHAPEIT | 0 | -0.0012041 | 1.69e-05 | 1202 | -71.3897344 | 0.0000000 | 7 |
| method | Beagle - Eagle | 0 | 0.0007321 | 1.95e-05 | 1202 | 37.5369195 | 0.0000000 | 8 |
| method | Beagle - SHAPEIT | 0 | -0.0005089 | 1.95e-05 | 1202 | -26.0961643 | 0.0000000 | 8 |
| method | Eagle - SHAPEIT | 0 | -0.0012410 | 1.95e-05 | 1202 | -63.6330838 | 0.0000000 | 8 |
| method | Beagle - Eagle | 0 | 0.0007718 | 1.84e-05 | 1202 | 41.9768441 | 0.0000000 | 9 |
| method | Beagle - SHAPEIT | 0 | -0.0005220 | 1.84e-05 | 1202 | -28.3888396 | 0.0000000 | 9 |
| method | Eagle - SHAPEIT | 0 | -0.0012938 | 1.84e-05 | 1202 | -70.3656836 | 0.0000000 | 9 |
| method | Beagle - Eagle | 0 | 0.0006935 | 1.71e-05 | 1202 | 40.4636630 | 0.0000000 | 10 |
| method | Beagle - SHAPEIT | 0 | -0.0004814 | 1.71e-05 | 1202 | -28.0897810 | 0.0000000 | 10 |
| method | Eagle - SHAPEIT | 0 | -0.0011749 | 1.71e-05 | 1202 | -68.5534440 | 0.0000000 | 10 |
| method | Beagle - Eagle | 0 | 0.0007285 | 1.82e-05 | 1202 | 39.9658214 | 0.0000000 | 11 |
| method | Beagle - SHAPEIT | 0 | -0.0004682 | 1.82e-05 | 1202 | -25.6840547 | 0.0000000 | 11 |
| method | Eagle - SHAPEIT | 0 | -0.0011967 | 1.82e-05 | 1202 | -65.6498761 | 0.0000000 | 11 |
| method | Beagle - Eagle | 0 | 0.0007410 | 1.86e-05 | 1202 | 39.8553280 | 0.0000000 | 12 |
| method | Beagle - SHAPEIT | 0 | -0.0005012 | 1.86e-05 | 1202 | -26.9579298 | 0.0000000 | 12 |
| method | Eagle - SHAPEIT | 0 | -0.0012422 | 1.86e-05 | 1202 | -66.8132578 | 0.0000000 | 12 |
| method | Beagle - Eagle | 0 | 0.0007003 | 2.05e-05 | 1202 | 34.1204928 | 0.0000000 | 13 |
| method | Beagle - SHAPEIT | 0 | -0.0004827 | 2.05e-05 | 1202 | -23.5186982 | 0.0000000 | 13 |
| method | Eagle - SHAPEIT | 0 | -0.0011831 | 2.05e-05 | 1202 | -57.6391910 | 0.0000000 | 13 |
| method | Beagle - Eagle | 0 | 0.0006995 | 1.98e-05 | 1202 | 35.2821507 | 0.0000000 | 14 |
| method | Beagle - SHAPEIT | 0 | -0.0005254 | 1.98e-05 | 1202 | -26.4993205 | 0.0000000 | 14 |
| method | Eagle - SHAPEIT | 0 | -0.0012249 | 1.98e-05 | 1202 | -61.7814712 | 0.0000000 | 14 |
| method | Beagle - Eagle | 0 | 0.0007213 | 2.05e-05 | 1202 | 35.1503531 | 0.0000000 | 15 |
| method | Beagle - SHAPEIT | 0 | -0.0005544 | 2.05e-05 | 1202 | -27.0170709 | 0.0000000 | 15 |
| method | Eagle - SHAPEIT | 0 | -0.0012757 | 2.05e-05 | 1202 | -62.1674240 | 0.0000000 | 15 |
| method | Beagle - Eagle | 0 | 0.0008699 | 2.40e-05 | 1202 | 36.2100322 | 0.0000000 | 16 |
| method | Beagle - SHAPEIT | 0 | -0.0005525 | 2.40e-05 | 1202 | -22.9956142 | 0.0000000 | 16 |
| method | Eagle - SHAPEIT | 0 | -0.0014224 | 2.40e-05 | 1202 | -59.2056464 | 0.0000000 | 16 |
| method | Beagle - Eagle | 0 | 0.0007498 | 2.27e-05 | 1202 | 33.0596397 | 0.0000000 | 17 |
| method | Beagle - SHAPEIT | 0 | -0.0005528 | 2.27e-05 | 1202 | -24.3747719 | 0.0000000 | 17 |
| method | Eagle - SHAPEIT | 0 | -0.0013026 | 2.27e-05 | 1202 | -57.4344116 | 0.0000000 | 17 |
| method | Beagle - Eagle | 0 | 0.0007255 | 2.01e-05 | 1202 | 36.0323784 | 0.0000000 | 18 |
| method | Beagle - SHAPEIT | 0 | -0.0005025 | 2.01e-05 | 1202 | -24.9571910 | 0.0000000 | 18 |
| method | Eagle - SHAPEIT | 0 | -0.0012280 | 2.01e-05 | 1202 | -60.9895694 | 0.0000000 | 18 |
| method | Beagle - Eagle | 0 | 0.0007466 | 2.28e-05 | 1202 | 32.8036707 | 0.0000000 | 19 |
| method | Beagle - SHAPEIT | 0 | -0.0004552 | 2.28e-05 | 1202 | -20.0009441 | 0.0000000 | 19 |
| method | Eagle - SHAPEIT | 0 | -0.0012018 | 2.28e-05 | 1202 | -52.8046148 | 0.0000000 | 19 |
| method | Beagle - Eagle | 0 | 0.0007164 | 2.28e-05 | 1202 | 31.4130234 | 0.0000000 | 20 |
| method | Beagle - SHAPEIT | 0 | -0.0004965 | 2.28e-05 | 1202 | -21.7698034 | 0.0000000 | 20 |
| method | Eagle - SHAPEIT | 0 | -0.0012129 | 2.28e-05 | 1202 | -53.1828268 | 0.0000000 | 20 |
| method | Beagle - Eagle | 0 | 0.0005952 | 2.52e-05 | 1202 | 23.5757485 | 0.0000000 | 21 |
| method | Beagle - SHAPEIT | 0 | -0.0005286 | 2.52e-05 | 1202 | -20.9358326 | 0.0000000 | 21 |
| method | Eagle - SHAPEIT | 0 | -0.0011238 | 2.52e-05 | 1202 | -44.5115811 | 0.0000000 | 21 |
| method | Beagle - Eagle | 0 | 0.0006212 | 2.76e-05 | 1202 | 22.4682068 | 0.0000000 | 22 |
| method | Beagle - SHAPEIT | 0 | -0.0005428 | 2.76e-05 | 1202 | -19.6324060 | 0.0000000 | 22 |
| method | Eagle - SHAPEIT | 0 | -0.0011640 | 2.76e-05 | 1202 | -42.1006129 | 0.0000000 | 22 |
| method | Beagle - Eagle | 0 | 0.0000045 | 5.90e-06 | 1998 | 0.7705121 | 0.7211872 | 23 |
| method | Beagle - SHAPEIT | 0 | -0.0001802 | 5.90e-06 | 1998 | -30.5670808 | 0.0000000 | 23 |
| method | Eagle - SHAPEIT | 0 | -0.0001848 | 5.90e-06 | 1998 | -31.3375929 | 0.0000000 | 23 |
mod_fit <- df_flips %>%
filter(chrom == 1) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
df_pop_anova <- anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = 1)
df_pop_pairwise <- emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=1)
df_pop_pop <- emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = 1)
for(i in 2:23){
mod_fit <- df_flips %>%
filter(chrom == i) %>%
pivot_longer(Eagle:SHAPEIT, names_to = "method", values_to = "error_rate") %>%
{lmerTest::lmer(error_rate ~ method*SUPER + (1|pair_id), data = .)}
df_pop_anova <- df_pop_anova %>% bind_rows({anova(mod_fit) %>% broom::tidy() %>% mutate(chrom = i)})
df_pop_pairwise <- df_pop_pairwise %>% bind_rows({
emmeans::emmeans(mod_fit, ~ method | SUPER) %>% pairs() %>% broom::tidy() %>% mutate(chrom=i)})
df_pop_pop <- df_pop_pop %>% bind_rows({
emmeans::emmeans(mod_fit, ~ SUPER | method) %>% pairs() %>% broom::tidy() %>% mutate(chrom = i)})
}
df_pop_anova %>%
knitr::kable()
| term | sumsq | meansq | NumDF | DenDF | statistic | p.value | chrom |
|---|---|---|---|---|---|---|---|
| method | 0.0003967 | 0.0001983 | 2 | 1194.0000 | 3192.826276 | 0.0000000 | 1 |
| SUPER | 0.0000276 | 0.0000069 | 4 | 597.0000 | 111.269503 | 0.0000000 | 1 |
| method:SUPER | 0.0000196 | 0.0000024 | 8 | 1194.0000 | 39.413286 | 0.0000000 | 1 |
| method | 0.0004588 | 0.0002294 | 2 | 1194.0000 | 3464.684510 | 0.0000000 | 2 |
| SUPER | 0.0000327 | 0.0000082 | 4 | 597.0000 | 123.522649 | 0.0000000 | 2 |
| method:SUPER | 0.0000178 | 0.0000022 | 8 | 1194.0000 | 33.617845 | 0.0000000 | 2 |
| method | 0.0003820 | 0.0001910 | 2 | 1194.0000 | 3181.378464 | 0.0000000 | 3 |
| SUPER | 0.0000271 | 0.0000068 | 4 | 597.0000 | 112.819852 | 0.0000000 | 3 |
| method:SUPER | 0.0000197 | 0.0000025 | 8 | 1194.0000 | 40.986641 | 0.0000000 | 3 |
| method | 0.0003275 | 0.0001637 | 2 | 1194.0000 | 2558.720305 | 0.0000000 | 4 |
| SUPER | 0.0000312 | 0.0000078 | 4 | 597.0000 | 121.768081 | 0.0000000 | 4 |
| method:SUPER | 0.0000148 | 0.0000018 | 8 | 1194.0000 | 28.856281 | 0.0000000 | 4 |
| method | 0.0003935 | 0.0001968 | 2 | 1194.0000 | 2891.005556 | 0.0000000 | 5 |
| SUPER | 0.0000287 | 0.0000072 | 4 | 597.0000 | 105.490039 | 0.0000000 | 5 |
| method:SUPER | 0.0000208 | 0.0000026 | 8 | 1194.0000 | 38.224530 | 0.0000000 | 5 |
| method | 0.0003006 | 0.0001503 | 2 | 1194.0000 | 2799.000055 | 0.0000000 | 6 |
| SUPER | 0.0000219 | 0.0000055 | 4 | 597.0000 | 101.834616 | 0.0000000 | 6 |
| method:SUPER | 0.0000160 | 0.0000020 | 8 | 1194.0000 | 37.296767 | 0.0000000 | 6 |
| method | 0.0003749 | 0.0001874 | 2 | 1194.0000 | 2578.764416 | 0.0000000 | 7 |
| SUPER | 0.0000327 | 0.0000082 | 4 | 597.0000 | 112.299606 | 0.0000000 | 7 |
| method:SUPER | 0.0000161 | 0.0000020 | 8 | 1194.0000 | 27.745892 | 0.0000000 | 7 |
| method | 0.0003851 | 0.0001926 | 2 | 1194.0000 | 2020.831393 | 0.0000000 | 8 |
| SUPER | 0.0000425 | 0.0000106 | 4 | 597.0000 | 111.515524 | 0.0000000 | 8 |
| method:SUPER | 0.0000238 | 0.0000030 | 8 | 1194.0000 | 31.262187 | 0.0000000 | 8 |
| method | 0.0004287 | 0.0002143 | 2 | 1194.0000 | 2538.806313 | 0.0000000 | 9 |
| SUPER | 0.0000345 | 0.0000086 | 4 | 597.0000 | 102.026700 | 0.0000000 | 9 |
| method:SUPER | 0.0000215 | 0.0000027 | 8 | 1194.0000 | 31.857680 | 0.0000000 | 9 |
| method | 0.0003517 | 0.0001759 | 2 | 1194.0000 | 2356.376792 | 0.0000000 | 10 |
| SUPER | 0.0000328 | 0.0000082 | 4 | 596.9999 | 109.877832 | 0.0000000 | 10 |
| method:SUPER | 0.0000172 | 0.0000021 | 8 | 1194.0000 | 28.739506 | 0.0000000 | 10 |
| method | 0.0003711 | 0.0001855 | 2 | 1194.0000 | 2178.697681 | 0.0000000 | 11 |
| SUPER | 0.0000366 | 0.0000091 | 4 | 597.0000 | 107.358104 | 0.0000000 | 11 |
| method:SUPER | 0.0000185 | 0.0000023 | 8 | 1194.0000 | 27.220855 | 0.0000000 | 11 |
| method | 0.0004031 | 0.0002016 | 2 | 1194.0000 | 2319.701014 | 0.0000000 | 12 |
| SUPER | 0.0000358 | 0.0000090 | 4 | 596.9999 | 103.017010 | 0.0000000 | 12 |
| method:SUPER | 0.0000213 | 0.0000027 | 8 | 1194.0000 | 30.677480 | 0.0000000 | 12 |
| method | 0.0003504 | 0.0001752 | 2 | 1194.0000 | 1535.886331 | 0.0000000 | 13 |
| SUPER | 0.0000432 | 0.0000108 | 4 | 597.0000 | 94.754693 | 0.0000000 | 13 |
| method:SUPER | 0.0000162 | 0.0000020 | 8 | 1194.0000 | 17.764775 | 0.0000000 | 13 |
| method | 0.0003811 | 0.0001906 | 2 | 1194.0000 | 1821.579291 | 0.0000000 | 14 |
| SUPER | 0.0000400 | 0.0000100 | 4 | 597.0000 | 95.492420 | 0.0000000 | 14 |
| method:SUPER | 0.0000173 | 0.0000022 | 8 | 1194.0000 | 20.672648 | 0.0000000 | 14 |
| method | 0.0004234 | 0.0002117 | 2 | 1194.0000 | 1858.557476 | 0.0000000 | 15 |
| SUPER | 0.0000414 | 0.0000104 | 4 | 597.0000 | 90.917098 | 0.0000000 | 15 |
| method:SUPER | 0.0000163 | 0.0000020 | 8 | 1194.0000 | 17.932999 | 0.0000000 | 15 |
| method | 0.0005389 | 0.0002695 | 2 | 1194.0000 | 1694.618761 | 0.0000000 | 16 |
| SUPER | 0.0000573 | 0.0000143 | 4 | 597.0000 | 90.099898 | 0.0000000 | 16 |
| method:SUPER | 0.0000190 | 0.0000024 | 8 | 1194.0000 | 14.913350 | 0.0000000 | 16 |
| method | 0.0004385 | 0.0002193 | 2 | 1194.0000 | 1515.063291 | 0.0000000 | 17 |
| SUPER | 0.0000544 | 0.0000136 | 4 | 597.0000 | 93.955710 | 0.0000000 | 17 |
| method:SUPER | 0.0000133 | 0.0000017 | 8 | 1194.0000 | 11.491384 | 0.0000000 | 17 |
| method | 0.0003825 | 0.0001913 | 2 | 1194.0000 | 1774.755328 | 0.0000000 | 18 |
| SUPER | 0.0000479 | 0.0000120 | 4 | 597.0000 | 111.168244 | 0.0000000 | 18 |
| method:SUPER | 0.0000180 | 0.0000023 | 8 | 1194.0000 | 20.880766 | 0.0000000 | 18 |
| method | 0.0003829 | 0.0001915 | 2 | 1194.0000 | 1337.730530 | 0.0000000 | 19 |
| SUPER | 0.0000500 | 0.0000125 | 4 | 597.0000 | 87.270523 | 0.0000000 | 19 |
| method:SUPER | 0.0000165 | 0.0000021 | 8 | 1194.0000 | 14.436580 | 0.0000000 | 19 |
| method | 0.0003781 | 0.0001890 | 2 | 1194.0000 | 1327.232824 | 0.0000000 | 20 |
| SUPER | 0.0000550 | 0.0000137 | 4 | 597.0000 | 96.500071 | 0.0000000 | 20 |
| method:SUPER | 0.0000181 | 0.0000023 | 8 | 1194.0000 | 15.887647 | 0.0000000 | 20 |
| method | 0.0003217 | 0.0001609 | 2 | 1194.0000 | 879.761890 | 0.0000000 | 21 |
| SUPER | 0.0000411 | 0.0000103 | 4 | 597.0000 | 56.153871 | 0.0000000 | 21 |
| method:SUPER | 0.0000123 | 0.0000015 | 8 | 1194.0000 | 8.418774 | 0.0000000 | 21 |
| method | 0.0003411 | 0.0001706 | 2 | 1194.0000 | 785.671346 | 0.0000000 | 22 |
| SUPER | 0.0000543 | 0.0000136 | 4 | 597.0000 | 62.530883 | 0.0000000 | 22 |
| method:SUPER | 0.0000173 | 0.0000022 | 8 | 1194.0000 | 9.977930 | 0.0000000 | 22 |
| method | 0.0000222 | 0.0000111 | 2 | 1990.0000 | 641.105027 | 0.0000000 | 23 |
| SUPER | 0.0000178 | 0.0000044 | 4 | 995.0000 | 256.572985 | 0.0000000 | 23 |
| method:SUPER | 0.0000003 | 0.0000000 | 8 | 1990.0000 | 1.824723 | 0.0681454 | 23 |
df_pop_pairwise %>% knitr::kable()
| SUPER | term | contrast | null.value | estimate | std.error | df | statistic | adj.p.value | chrom |
|---|---|---|---|---|---|---|---|---|---|
| AFR | method | Beagle - Eagle | 0 | 0.0009903 | 2.49e-05 | 1194 | 39.8313731 | 0.0000000 | 1 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004435 | 2.49e-05 | 1194 | -17.8370961 | 0.0000000 | 1 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0014338 | 2.49e-05 | 1194 | -57.6684692 | 0.0000000 | 1 |
| AMR | method | Beagle - Eagle | 0 | 0.0005874 | 3.01e-05 | 1194 | 19.5069897 | 0.0000000 | 1 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005642 | 3.01e-05 | 1194 | -18.7336247 | 0.0000000 | 1 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0011516 | 3.01e-05 | 1194 | -38.2406145 | 0.0000000 | 1 |
| EAS | method | Beagle - Eagle | 0 | 0.0006869 | 4.15e-05 | 1194 | 16.5360004 | 0.0000000 | 1 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005172 | 4.15e-05 | 1194 | -12.4506624 | 0.0000000 | 1 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0012041 | 4.15e-05 | 1194 | -28.9866628 | 0.0000000 | 1 |
| EUR | method | Beagle - Eagle | 0 | 0.0004829 | 3.41e-05 | 1194 | 14.1700951 | 0.0000000 | 1 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003613 | 3.41e-05 | 1194 | -10.6031851 | 0.0000000 | 1 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008442 | 3.41e-05 | 1194 | -24.7732801 | 0.0000000 | 1 |
| SAS | method | Beagle - Eagle | 0 | 0.0007945 | 3.82e-05 | 1194 | 20.7802550 | 0.0000000 | 1 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006696 | 3.82e-05 | 1194 | -17.5129608 | 0.0000000 | 1 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0014640 | 3.82e-05 | 1194 | -38.2932157 | 0.0000000 | 1 |
| AFR | method | Beagle - Eagle | 0 | 0.0010298 | 2.57e-05 | 1194 | 40.1220106 | 0.0000000 | 2 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004682 | 2.57e-05 | 1194 | -18.2433930 | 0.0000000 | 2 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0014980 | 2.57e-05 | 1194 | -58.3654037 | 0.0000000 | 2 |
| AMR | method | Beagle - Eagle | 0 | 0.0006658 | 3.11e-05 | 1194 | 21.4151192 | 0.0000000 | 2 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005254 | 3.11e-05 | 1194 | -16.9002652 | 0.0000000 | 2 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0011912 | 3.11e-05 | 1194 | -38.3153843 | 0.0000000 | 2 |
| EAS | method | Beagle - Eagle | 0 | 0.0006921 | 4.29e-05 | 1194 | 16.1382729 | 0.0000000 | 2 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006601 | 4.29e-05 | 1194 | -15.3916948 | 0.0000000 | 2 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0013521 | 4.29e-05 | 1194 | -31.5299677 | 0.0000000 | 2 |
| EUR | method | Beagle - Eagle | 0 | 0.0005449 | 3.52e-05 | 1194 | 15.4903048 | 0.0000000 | 2 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0004166 | 3.52e-05 | 1194 | -11.8414627 | 0.0000000 | 2 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0009615 | 3.52e-05 | 1194 | -27.3317674 | 0.0000000 | 2 |
| SAS | method | Beagle - Eagle | 0 | 0.0008948 | 3.95e-05 | 1194 | 22.6702712 | 0.0000000 | 2 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006577 | 3.95e-05 | 1194 | -16.6646840 | 0.0000000 | 2 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0015525 | 3.95e-05 | 1194 | -39.3349552 | 0.0000000 | 2 |
| AFR | method | Beagle - Eagle | 0 | 0.0009951 | 2.44e-05 | 1194 | 40.7119464 | 0.0000000 | 3 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004516 | 2.44e-05 | 1194 | -18.4748575 | 0.0000000 | 3 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0014466 | 2.44e-05 | 1194 | -59.1868040 | 0.0000000 | 3 |
| AMR | method | Beagle - Eagle | 0 | 0.0005918 | 2.96e-05 | 1194 | 19.9906523 | 0.0000000 | 3 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005198 | 2.96e-05 | 1194 | -17.5587685 | 0.0000000 | 3 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0011117 | 2.96e-05 | 1194 | -37.5494207 | 0.0000000 | 3 |
| EAS | method | Beagle - Eagle | 0 | 0.0006620 | 4.08e-05 | 1194 | 16.2104761 | 0.0000000 | 3 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005101 | 4.08e-05 | 1194 | -12.4908586 | 0.0000000 | 3 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0011721 | 4.08e-05 | 1194 | -28.7013347 | 0.0000000 | 3 |
| EUR | method | Beagle - Eagle | 0 | 0.0004726 | 3.35e-05 | 1194 | 14.1075643 | 0.0000000 | 3 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003646 | 3.35e-05 | 1194 | -10.8842658 | 0.0000000 | 3 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008372 | 3.35e-05 | 1194 | -24.9918301 | 0.0000000 | 3 |
| SAS | method | Beagle - Eagle | 0 | 0.0007816 | 3.76e-05 | 1194 | 20.7940464 | 0.0000000 | 3 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006314 | 3.76e-05 | 1194 | -16.8001160 | 0.0000000 | 3 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0014130 | 3.76e-05 | 1194 | -37.5941624 | 0.0000000 | 3 |
| AFR | method | Beagle - Eagle | 0 | 0.0009142 | 2.52e-05 | 1194 | 36.2285157 | 0.0000000 | 4 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003938 | 2.52e-05 | 1194 | -15.6048424 | 0.0000000 | 4 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0013079 | 2.52e-05 | 1194 | -51.8333581 | 0.0000000 | 4 |
| AMR | method | Beagle - Eagle | 0 | 0.0005299 | 3.06e-05 | 1194 | 17.3368943 | 0.0000000 | 4 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005104 | 3.06e-05 | 1194 | -16.6995945 | 0.0000000 | 4 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0010403 | 3.06e-05 | 1194 | -34.0364888 | 0.0000000 | 4 |
| EAS | method | Beagle - Eagle | 0 | 0.0005373 | 4.22e-05 | 1194 | 12.7438226 | 0.0000000 | 4 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005674 | 4.22e-05 | 1194 | -13.4574360 | 0.0000000 | 4 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0011047 | 4.22e-05 | 1194 | -26.2012585 | 0.0000000 | 4 |
| EUR | method | Beagle - Eagle | 0 | 0.0004620 | 3.46e-05 | 1194 | 13.3594147 | 0.0000000 | 4 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003554 | 3.46e-05 | 1194 | -10.2758253 | 0.0000000 | 4 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008174 | 3.46e-05 | 1194 | -23.6352400 | 0.0000000 | 4 |
| SAS | method | Beagle - Eagle | 0 | 0.0007459 | 3.88e-05 | 1194 | 19.2217748 | 0.0000000 | 4 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0005272 | 3.88e-05 | 1194 | -13.5866435 | 0.0000000 | 4 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0012731 | 3.88e-05 | 1194 | -32.8084183 | 0.0000000 | 4 |
| AFR | method | Beagle - Eagle | 0 | 0.0009939 | 2.60e-05 | 1194 | 38.1919929 | 0.0000000 | 5 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004369 | 2.60e-05 | 1194 | -16.7895457 | 0.0000000 | 5 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0014308 | 2.60e-05 | 1194 | -54.9815386 | 0.0000000 | 5 |
| AMR | method | Beagle - Eagle | 0 | 0.0005264 | 3.15e-05 | 1194 | 16.6998560 | 0.0000000 | 5 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005608 | 3.15e-05 | 1194 | -17.7900173 | 0.0000000 | 5 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0010872 | 3.15e-05 | 1194 | -34.4898733 | 0.0000000 | 5 |
| EAS | method | Beagle - Eagle | 0 | 0.0006602 | 4.35e-05 | 1194 | 15.1833345 | 0.0000000 | 5 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006254 | 4.35e-05 | 1194 | -14.3823834 | 0.0000000 | 5 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0012856 | 4.35e-05 | 1194 | -29.5657179 | 0.0000000 | 5 |
| EUR | method | Beagle - Eagle | 0 | 0.0004922 | 3.57e-05 | 1194 | 13.8001126 | 0.0000000 | 5 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003560 | 3.57e-05 | 1194 | -9.9820022 | 0.0000000 | 5 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008483 | 3.57e-05 | 1194 | -23.7821148 | 0.0000000 | 5 |
| SAS | method | Beagle - Eagle | 0 | 0.0008086 | 4.00e-05 | 1194 | 20.2052594 | 0.0000000 | 5 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006180 | 4.00e-05 | 1194 | -15.4439938 | 0.0000000 | 5 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0014266 | 4.00e-05 | 1194 | -35.6492532 | 0.0000000 | 5 |
| AFR | method | Beagle - Eagle | 0 | 0.0008863 | 2.31e-05 | 1194 | 38.3462428 | 0.0000000 | 6 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0003968 | 2.31e-05 | 1194 | -17.1692991 | 0.0000000 | 6 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0012832 | 2.31e-05 | 1194 | -55.5155419 | 0.0000000 | 6 |
| AMR | method | Beagle - Eagle | 0 | 0.0004764 | 2.80e-05 | 1194 | 17.0174981 | 0.0000000 | 6 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0004563 | 2.80e-05 | 1194 | -16.2991758 | 0.0000000 | 6 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0009328 | 2.80e-05 | 1194 | -33.3166740 | 0.0000000 | 6 |
| EAS | method | Beagle - Eagle | 0 | 0.0006098 | 3.86e-05 | 1194 | 15.7914101 | 0.0000000 | 6 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0004639 | 3.86e-05 | 1194 | -12.0122281 | 0.0000000 | 6 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0010737 | 3.86e-05 | 1194 | -27.8036382 | 0.0000000 | 6 |
| EUR | method | Beagle - Eagle | 0 | 0.0004486 | 3.17e-05 | 1194 | 14.1608269 | 0.0000000 | 6 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003083 | 3.17e-05 | 1194 | -9.7326504 | 0.0000000 | 6 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0007569 | 3.17e-05 | 1194 | -23.8934773 | 0.0000000 | 6 |
| SAS | method | Beagle - Eagle | 0 | 0.0007196 | 3.55e-05 | 1194 | 20.2457655 | 0.0000000 | 6 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0005344 | 3.55e-05 | 1194 | -15.0363649 | 0.0000000 | 6 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0012540 | 3.55e-05 | 1194 | -35.2821303 | 0.0000000 | 6 |
| AFR | method | Beagle - Eagle | 0 | 0.0008938 | 2.69e-05 | 1194 | 33.2346534 | 0.0000000 | 7 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0005032 | 2.69e-05 | 1194 | -18.7094220 | 0.0000000 | 7 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0013969 | 2.69e-05 | 1194 | -51.9440755 | 0.0000000 | 7 |
| AMR | method | Beagle - Eagle | 0 | 0.0005815 | 3.26e-05 | 1194 | 17.8518350 | 0.0000000 | 7 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0004904 | 3.26e-05 | 1194 | -15.0550500 | 0.0000000 | 7 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0010719 | 3.26e-05 | 1194 | -32.9068849 | 0.0000000 | 7 |
| EAS | method | Beagle - Eagle | 0 | 0.0006870 | 4.49e-05 | 1194 | 15.2899737 | 0.0000000 | 7 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005133 | 4.49e-05 | 1194 | -11.4239565 | 0.0000000 | 7 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0012004 | 4.49e-05 | 1194 | -26.7139302 | 0.0000000 | 7 |
| EUR | method | Beagle - Eagle | 0 | 0.0004524 | 3.69e-05 | 1194 | 12.2724546 | 0.0000000 | 7 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003840 | 3.69e-05 | 1194 | -10.4192855 | 0.0000000 | 7 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008364 | 3.69e-05 | 1194 | -22.6917401 | 0.0000000 | 7 |
| SAS | method | Beagle - Eagle | 0 | 0.0007833 | 4.14e-05 | 1194 | 18.9413622 | 0.0000000 | 7 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006436 | 4.14e-05 | 1194 | -15.5630446 | 0.0000000 | 7 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0014269 | 4.14e-05 | 1194 | -34.5044068 | 0.0000000 | 7 |
| AFR | method | Beagle - Eagle | 0 | 0.0010102 | 3.08e-05 | 1194 | 32.8076986 | 0.0000000 | 8 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004951 | 3.08e-05 | 1194 | -16.0769328 | 0.0000000 | 8 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0015053 | 3.08e-05 | 1194 | -48.8846314 | 0.0000000 | 8 |
| AMR | method | Beagle - Eagle | 0 | 0.0005199 | 3.73e-05 | 1194 | 13.9391027 | 0.0000000 | 8 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005939 | 3.73e-05 | 1194 | -15.9235135 | 0.0000000 | 8 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0011138 | 3.73e-05 | 1194 | -29.8626162 | 0.0000000 | 8 |
| EAS | method | Beagle - Eagle | 0 | 0.0006985 | 5.14e-05 | 1194 | 13.5757631 | 0.0000000 | 8 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0004364 | 5.14e-05 | 1194 | -8.4815494 | 0.0000000 | 8 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0011348 | 5.14e-05 | 1194 | -22.0573125 | 0.0000000 | 8 |
| EUR | method | Beagle - Eagle | 0 | 0.0004753 | 4.22e-05 | 1194 | 11.2625084 | 0.0000000 | 8 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003626 | 4.22e-05 | 1194 | -8.5912484 | 0.0000000 | 8 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008379 | 4.22e-05 | 1194 | -19.8537569 | 0.0000000 | 8 |
| SAS | method | Beagle - Eagle | 0 | 0.0007679 | 4.74e-05 | 1194 | 16.2171959 | 0.0000000 | 8 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006506 | 4.74e-05 | 1194 | -13.7388077 | 0.0000000 | 8 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0014185 | 4.74e-05 | 1194 | -29.9560036 | 0.0000000 | 8 |
| AFR | method | Beagle - Eagle | 0 | 0.0010093 | 2.90e-05 | 1194 | 34.8231128 | 0.0000000 | 9 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0005144 | 2.90e-05 | 1194 | -17.7462965 | 0.0000000 | 9 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0015237 | 2.90e-05 | 1194 | -52.5694093 | 0.0000000 | 9 |
| AMR | method | Beagle - Eagle | 0 | 0.0005949 | 3.51e-05 | 1194 | 16.9440156 | 0.0000000 | 9 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005796 | 3.51e-05 | 1194 | -16.5105705 | 0.0000000 | 9 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0011745 | 3.51e-05 | 1194 | -33.4545861 | 0.0000000 | 9 |
| EAS | method | Beagle - Eagle | 0 | 0.0007375 | 4.84e-05 | 1194 | 15.2281265 | 0.0000000 | 9 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005346 | 4.84e-05 | 1194 | -11.0390979 | 0.0000000 | 9 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0012721 | 4.84e-05 | 1194 | -26.2672245 | 0.0000000 | 9 |
| EUR | method | Beagle - Eagle | 0 | 0.0005257 | 3.97e-05 | 1194 | 13.2338941 | 0.0000000 | 9 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003380 | 3.97e-05 | 1194 | -8.5076843 | 0.0000000 | 9 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008637 | 3.97e-05 | 1194 | -21.7415784 | 0.0000000 | 9 |
| SAS | method | Beagle - Eagle | 0 | 0.0008345 | 4.46e-05 | 1194 | 18.7234833 | 0.0000000 | 9 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006681 | 4.46e-05 | 1194 | -14.9905111 | 0.0000000 | 9 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0015027 | 4.46e-05 | 1194 | -33.7139944 | 0.0000000 | 9 |
| AFR | method | Beagle - Eagle | 0 | 0.0009361 | 2.73e-05 | 1194 | 34.3517583 | 0.0000000 | 10 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004540 | 2.73e-05 | 1194 | -16.6621745 | 0.0000000 | 10 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0013901 | 2.73e-05 | 1194 | -51.0139328 | 0.0000000 | 10 |
| AMR | method | Beagle - Eagle | 0 | 0.0005421 | 3.30e-05 | 1194 | 16.4240841 | 0.0000000 | 10 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005065 | 3.30e-05 | 1194 | -15.3439172 | 0.0000000 | 10 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0010486 | 3.30e-05 | 1194 | -31.7680013 | 0.0000000 | 10 |
| EAS | method | Beagle - Eagle | 0 | 0.0006121 | 4.55e-05 | 1194 | 13.4448458 | 0.0000000 | 10 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005552 | 4.55e-05 | 1194 | -12.1934201 | 0.0000000 | 10 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0011673 | 4.55e-05 | 1194 | -25.6382660 | 0.0000000 | 10 |
| EUR | method | Beagle - Eagle | 0 | 0.0004820 | 3.73e-05 | 1194 | 12.9047204 | 0.0000000 | 10 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003389 | 3.73e-05 | 1194 | -9.0728078 | 0.0000000 | 10 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008208 | 3.73e-05 | 1194 | -21.9775282 | 0.0000000 | 10 |
| SAS | method | Beagle - Eagle | 0 | 0.0006988 | 4.19e-05 | 1194 | 16.6755787 | 0.0000000 | 10 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006227 | 4.19e-05 | 1194 | -14.8589263 | 0.0000000 | 10 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0013214 | 4.19e-05 | 1194 | -31.5345050 | 0.0000000 | 10 |
| AFR | method | Beagle - Eagle | 0 | 0.0009588 | 2.91e-05 | 1194 | 32.9384553 | 0.0000000 | 11 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004442 | 2.91e-05 | 1194 | -15.2588026 | 0.0000000 | 11 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0014030 | 2.91e-05 | 1194 | -48.1972579 | 0.0000000 | 11 |
| AMR | method | Beagle - Eagle | 0 | 0.0005846 | 3.53e-05 | 1194 | 16.5804633 | 0.0000000 | 11 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0004818 | 3.53e-05 | 1194 | -13.6655230 | 0.0000000 | 11 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0010664 | 3.53e-05 | 1194 | -30.2459863 | 0.0000000 | 11 |
| EAS | method | Beagle - Eagle | 0 | 0.0006792 | 4.86e-05 | 1194 | 13.9649322 | 0.0000000 | 11 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005654 | 4.86e-05 | 1194 | -11.6244214 | 0.0000000 | 11 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0012445 | 4.86e-05 | 1194 | -25.5893536 | 0.0000000 | 11 |
| EUR | method | Beagle - Eagle | 0 | 0.0004581 | 3.99e-05 | 1194 | 11.4830061 | 0.0000000 | 11 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003449 | 3.99e-05 | 1194 | -8.6454033 | 0.0000000 | 11 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008030 | 3.99e-05 | 1194 | -20.1284095 | 0.0000000 | 11 |
| SAS | method | Beagle - Eagle | 0 | 0.0007981 | 4.48e-05 | 1194 | 17.8298992 | 0.0000000 | 11 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0005758 | 4.48e-05 | 1194 | -12.8646792 | 0.0000000 | 11 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0013739 | 4.48e-05 | 1194 | -30.6945783 | 0.0000000 | 11 |
| AFR | method | Beagle - Eagle | 0 | 0.0009805 | 2.94e-05 | 1194 | 33.3456546 | 0.0000000 | 12 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004469 | 2.94e-05 | 1194 | -15.1973596 | 0.0000000 | 12 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0014273 | 2.94e-05 | 1194 | -48.5430142 | 0.0000000 | 12 |
| AMR | method | Beagle - Eagle | 0 | 0.0005527 | 3.56e-05 | 1194 | 15.5188460 | 0.0000000 | 12 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005160 | 3.56e-05 | 1194 | -14.4882119 | 0.0000000 | 12 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0010687 | 3.56e-05 | 1194 | -30.0070579 | 0.0000000 | 12 |
| EAS | method | Beagle - Eagle | 0 | 0.0006446 | 4.91e-05 | 1194 | 13.1209540 | 0.0000000 | 12 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005542 | 4.91e-05 | 1194 | -11.2813808 | 0.0000000 | 12 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0011989 | 4.91e-05 | 1194 | -24.4023348 | 0.0000000 | 12 |
| EUR | method | Beagle - Eagle | 0 | 0.0004945 | 4.03e-05 | 1194 | 12.2707447 | 0.0000000 | 12 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003928 | 4.03e-05 | 1194 | -9.7460039 | 0.0000000 | 12 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008873 | 4.03e-05 | 1194 | -22.0167485 | 0.0000000 | 12 |
| SAS | method | Beagle - Eagle | 0 | 0.0008702 | 4.52e-05 | 1194 | 19.2460888 | 0.0000000 | 12 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006976 | 4.52e-05 | 1194 | -15.4274222 | 0.0000000 | 12 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0015678 | 4.52e-05 | 1194 | -34.6735111 | 0.0000000 | 12 |
| AFR | method | Beagle - Eagle | 0 | 0.0009494 | 3.37e-05 | 1194 | 28.1796848 | 0.0000000 | 13 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004423 | 3.37e-05 | 1194 | -13.1289115 | 0.0000000 | 13 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0013918 | 3.37e-05 | 1194 | -41.3085963 | 0.0000000 | 13 |
| AMR | method | Beagle - Eagle | 0 | 0.0006155 | 4.08e-05 | 1194 | 15.0829186 | 0.0000000 | 13 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005177 | 4.08e-05 | 1194 | -12.6859367 | 0.0000000 | 13 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0011332 | 4.08e-05 | 1194 | -27.7688553 | 0.0000000 | 13 |
| EAS | method | Beagle - Eagle | 0 | 0.0006017 | 5.63e-05 | 1194 | 10.6882067 | 0.0000000 | 13 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005137 | 5.63e-05 | 1194 | -9.1248408 | 0.0000000 | 13 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0011153 | 5.63e-05 | 1194 | -19.8130475 | 0.0000000 | 13 |
| EUR | method | Beagle - Eagle | 0 | 0.0005105 | 4.62e-05 | 1194 | 11.0549581 | 0.0000000 | 13 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003295 | 4.62e-05 | 1194 | -7.1348827 | 0.0000000 | 13 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008400 | 4.62e-05 | 1194 | -18.1898408 | 0.0000000 | 13 |
| SAS | method | Beagle - Eagle | 0 | 0.0005706 | 5.18e-05 | 1194 | 11.0132829 | 0.0000000 | 13 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006886 | 5.18e-05 | 1194 | -13.2912596 | 0.0000000 | 13 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0012592 | 5.18e-05 | 1194 | -24.3045425 | 0.0000000 | 13 |
| AFR | method | Beagle - Eagle | 0 | 0.0009366 | 3.23e-05 | 1194 | 29.0277377 | 0.0000000 | 14 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004754 | 3.23e-05 | 1194 | -14.7358601 | 0.0000000 | 14 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0014120 | 3.23e-05 | 1194 | -43.7635978 | 0.0000000 | 14 |
| AMR | method | Beagle - Eagle | 0 | 0.0006184 | 3.91e-05 | 1194 | 15.8231990 | 0.0000000 | 14 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005319 | 3.91e-05 | 1194 | -13.6113316 | 0.0000000 | 14 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0011503 | 3.91e-05 | 1194 | -29.4345306 | 0.0000000 | 14 |
| EAS | method | Beagle - Eagle | 0 | 0.0005311 | 5.39e-05 | 1194 | 9.8515468 | 0.0000000 | 14 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006087 | 5.39e-05 | 1194 | -11.2908917 | 0.0000000 | 14 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0011398 | 5.39e-05 | 1194 | -21.1424385 | 0.0000000 | 14 |
| EUR | method | Beagle - Eagle | 0 | 0.0004178 | 4.42e-05 | 1194 | 9.4470466 | 0.0000000 | 14 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0004479 | 4.42e-05 | 1194 | -10.1290810 | 0.0000000 | 14 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008657 | 4.42e-05 | 1194 | -19.5761276 | 0.0000000 | 14 |
| SAS | method | Beagle - Eagle | 0 | 0.0007671 | 4.96e-05 | 1194 | 15.4608902 | 0.0000000 | 14 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006599 | 4.96e-05 | 1194 | -13.2999178 | 0.0000000 | 14 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0014270 | 4.96e-05 | 1194 | -28.7608080 | 0.0000000 | 14 |
| AFR | method | Beagle - Eagle | 0 | 0.0009330 | 3.37e-05 | 1194 | 27.7137999 | 0.0000000 | 15 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004976 | 3.37e-05 | 1194 | -14.7796766 | 0.0000000 | 15 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0014306 | 3.37e-05 | 1194 | -42.4934765 | 0.0000000 | 15 |
| AMR | method | Beagle - Eagle | 0 | 0.0006078 | 4.08e-05 | 1194 | 14.9045348 | 0.0000000 | 15 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005884 | 4.08e-05 | 1194 | -14.4299566 | 0.0000000 | 15 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0011962 | 4.08e-05 | 1194 | -29.3344915 | 0.0000000 | 15 |
| EAS | method | Beagle - Eagle | 0 | 0.0006875 | 5.63e-05 | 1194 | 12.2219924 | 0.0000000 | 15 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006197 | 5.63e-05 | 1194 | -11.0173355 | 0.0000000 | 15 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0013072 | 5.63e-05 | 1194 | -23.2393278 | 0.0000000 | 15 |
| EUR | method | Beagle - Eagle | 0 | 0.0004948 | 4.61e-05 | 1194 | 10.7222326 | 0.0000000 | 15 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0004012 | 4.61e-05 | 1194 | -8.6953236 | 0.0000000 | 15 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008960 | 4.61e-05 | 1194 | -19.4175562 | 0.0000000 | 15 |
| SAS | method | Beagle - Eagle | 0 | 0.0007174 | 5.18e-05 | 1194 | 13.8571011 | 0.0000000 | 15 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0007714 | 5.18e-05 | 1194 | -14.9000610 | 0.0000000 | 15 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0014888 | 5.18e-05 | 1194 | -28.7571621 | 0.0000000 | 15 |
| AFR | method | Beagle - Eagle | 0 | 0.0010336 | 3.98e-05 | 1194 | 25.9845228 | 0.0000000 | 16 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0005083 | 3.98e-05 | 1194 | -12.7796384 | 0.0000000 | 16 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0015419 | 3.98e-05 | 1194 | -38.7641612 | 0.0000000 | 16 |
| AMR | method | Beagle - Eagle | 0 | 0.0007562 | 4.82e-05 | 1194 | 15.6958664 | 0.0000000 | 16 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005972 | 4.82e-05 | 1194 | -12.3948802 | 0.0000000 | 16 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0013534 | 4.82e-05 | 1194 | -28.0907466 | 0.0000000 | 16 |
| EAS | method | Beagle - Eagle | 0 | 0.0008779 | 6.65e-05 | 1194 | 13.2097841 | 0.0000000 | 16 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005257 | 6.65e-05 | 1194 | -7.9102447 | 0.0000000 | 16 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0014036 | 6.65e-05 | 1194 | -21.1200288 | 0.0000000 | 16 |
| EUR | method | Beagle - Eagle | 0 | 0.0004868 | 5.45e-05 | 1194 | 8.9291526 | 0.0000000 | 16 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0005622 | 5.45e-05 | 1194 | -10.3117112 | 0.0000000 | 16 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0010490 | 5.45e-05 | 1194 | -19.2408638 | 0.0000000 | 16 |
| SAS | method | Beagle - Eagle | 0 | 0.0011418 | 6.12e-05 | 1194 | 18.6669233 | 0.0000000 | 16 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0005952 | 6.12e-05 | 1194 | -9.7305849 | 0.0000000 | 16 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0017370 | 6.12e-05 | 1194 | -28.3975082 | 0.0000000 | 16 |
| AFR | method | Beagle - Eagle | 0 | 0.0009037 | 3.79e-05 | 1194 | 23.8142970 | 0.0000000 | 17 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0005704 | 3.79e-05 | 1194 | -15.0312054 | 0.0000000 | 17 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0014741 | 3.79e-05 | 1194 | -38.8455023 | 0.0000000 | 17 |
| AMR | method | Beagle - Eagle | 0 | 0.0006554 | 4.60e-05 | 1194 | 14.2596925 | 0.0000000 | 17 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005576 | 4.60e-05 | 1194 | -12.1300782 | 0.0000000 | 17 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0012130 | 4.60e-05 | 1194 | -26.3897707 | 0.0000000 | 17 |
| EAS | method | Beagle - Eagle | 0 | 0.0007784 | 6.34e-05 | 1194 | 12.2766615 | 0.0000000 | 17 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0004861 | 6.34e-05 | 1194 | -7.6671341 | 0.0000000 | 17 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0012645 | 6.34e-05 | 1194 | -19.9437956 | 0.0000000 | 17 |
| EUR | method | Beagle - Eagle | 0 | 0.0005344 | 5.20e-05 | 1194 | 10.2753905 | 0.0000000 | 17 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0004193 | 5.20e-05 | 1194 | -8.0618827 | 0.0000000 | 17 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0009537 | 5.20e-05 | 1194 | -18.3372732 | 0.0000000 | 17 |
| SAS | method | Beagle - Eagle | 0 | 0.0007848 | 5.84e-05 | 1194 | 13.4487008 | 0.0000000 | 17 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0007282 | 5.84e-05 | 1194 | -12.4784645 | 0.0000000 | 17 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0015130 | 5.84e-05 | 1194 | -25.9271653 | 0.0000000 | 17 |
| AFR | method | Beagle - Eagle | 0 | 0.0009311 | 3.27e-05 | 1194 | 28.4332267 | 0.0000000 | 18 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0005011 | 3.27e-05 | 1194 | -15.3030643 | 0.0000000 | 18 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0014322 | 3.27e-05 | 1194 | -43.7362910 | 0.0000000 | 18 |
| AMR | method | Beagle - Eagle | 0 | 0.0006152 | 3.97e-05 | 1194 | 15.5104234 | 0.0000000 | 18 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005582 | 3.97e-05 | 1194 | -14.0743641 | 0.0000000 | 18 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0011735 | 3.97e-05 | 1194 | -29.5847874 | 0.0000000 | 18 |
| EAS | method | Beagle - Eagle | 0 | 0.0006572 | 5.47e-05 | 1194 | 12.0110972 | 0.0000000 | 18 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0004812 | 5.47e-05 | 1194 | -8.7954706 | 0.0000000 | 18 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0011384 | 5.47e-05 | 1194 | -20.8065678 | 0.0000000 | 18 |
| EUR | method | Beagle - Eagle | 0 | 0.0004612 | 4.49e-05 | 1194 | 10.2768356 | 0.0000000 | 18 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003517 | 4.49e-05 | 1194 | -7.8361100 | 0.0000000 | 18 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008129 | 4.49e-05 | 1194 | -18.1129456 | 0.0000000 | 18 |
| SAS | method | Beagle - Eagle | 0 | 0.0008077 | 5.04e-05 | 1194 | 16.0393063 | 0.0000000 | 18 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006238 | 5.04e-05 | 1194 | -12.3879880 | 0.0000000 | 18 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0014315 | 5.04e-05 | 1194 | -28.4272943 | 0.0000000 | 18 |
| AFR | method | Beagle - Eagle | 0 | 0.0009500 | 3.77e-05 | 1194 | 25.1730555 | 0.0000000 | 19 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004197 | 3.77e-05 | 1194 | -11.1219244 | 0.0000000 | 19 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0013697 | 3.77e-05 | 1194 | -36.2949798 | 0.0000000 | 19 |
| AMR | method | Beagle - Eagle | 0 | 0.0005645 | 4.57e-05 | 1194 | 12.3499532 | 0.0000000 | 19 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0004922 | 4.57e-05 | 1194 | -10.7689680 | 0.0000000 | 19 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0010567 | 4.57e-05 | 1194 | -23.1189212 | 0.0000000 | 19 |
| EAS | method | Beagle - Eagle | 0 | 0.0007675 | 6.31e-05 | 1194 | 12.1723495 | 0.0000000 | 19 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005041 | 6.31e-05 | 1194 | -7.9943179 | 0.0000000 | 19 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0012715 | 6.31e-05 | 1194 | -20.1666674 | 0.0000000 | 19 |
| EUR | method | Beagle - Eagle | 0 | 0.0005255 | 5.17e-05 | 1194 | 10.1592207 | 0.0000000 | 19 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0003221 | 5.17e-05 | 1194 | -6.2279019 | 0.0000000 | 19 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008476 | 5.17e-05 | 1194 | -16.3871226 | 0.0000000 | 19 |
| SAS | method | Beagle - Eagle | 0 | 0.0008199 | 5.80e-05 | 1194 | 14.1290024 | 0.0000000 | 19 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006057 | 5.80e-05 | 1194 | -10.4371748 | 0.0000000 | 19 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0014256 | 5.80e-05 | 1194 | -24.5661771 | 0.0000000 | 19 |
| AFR | method | Beagle - Eagle | 0 | 0.0009503 | 3.76e-05 | 1194 | 25.2430068 | 0.0000000 | 20 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0004275 | 3.76e-05 | 1194 | -11.3546946 | 0.0000000 | 20 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0013778 | 3.76e-05 | 1194 | -36.5977015 | 0.0000000 | 20 |
| AMR | method | Beagle - Eagle | 0 | 0.0006303 | 4.56e-05 | 1194 | 13.8225493 | 0.0000000 | 20 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005541 | 4.56e-05 | 1194 | -12.1503575 | 0.0000000 | 20 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0011844 | 4.56e-05 | 1194 | -25.9729068 | 0.0000000 | 20 |
| EAS | method | Beagle - Eagle | 0 | 0.0006016 | 6.29e-05 | 1194 | 9.5633759 | 0.0000000 | 20 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0006022 | 6.29e-05 | 1194 | -9.5734425 | 0.0000000 | 20 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0012037 | 6.29e-05 | 1194 | -19.1368184 | 0.0000000 | 20 |
| EUR | method | Beagle - Eagle | 0 | 0.0004010 | 5.16e-05 | 1194 | 7.7713077 | 0.0000000 | 20 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0004030 | 5.16e-05 | 1194 | -7.8097288 | 0.0000000 | 20 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008040 | 5.16e-05 | 1194 | -15.5810365 | 0.0000000 | 20 |
| SAS | method | Beagle - Eagle | 0 | 0.0007963 | 5.79e-05 | 1194 | 13.7553409 | 0.0000000 | 20 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0005950 | 5.79e-05 | 1194 | -10.2781881 | 0.0000000 | 20 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0013913 | 5.79e-05 | 1194 | -24.0335290 | 0.0000000 | 20 |
| AFR | method | Beagle - Eagle | 0 | 0.0007936 | 4.27e-05 | 1194 | 18.6063616 | 0.0000000 | 21 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0005259 | 4.27e-05 | 1194 | -12.3286685 | 0.0000000 | 21 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0013195 | 4.27e-05 | 1194 | -30.9350301 | 0.0000000 | 21 |
| AMR | method | Beagle - Eagle | 0 | 0.0004138 | 5.17e-05 | 1194 | 8.0095312 | 0.0000000 | 21 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005427 | 5.17e-05 | 1194 | -10.5038851 | 0.0000000 | 21 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0009565 | 5.17e-05 | 1194 | -18.5134163 | 0.0000000 | 21 |
| EAS | method | Beagle - Eagle | 0 | 0.0006084 | 7.13e-05 | 1194 | 8.5367065 | 0.0000000 | 21 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0004902 | 7.13e-05 | 1194 | -6.8790138 | 0.0000000 | 21 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0010986 | 7.13e-05 | 1194 | -15.4157203 | 0.0000000 | 21 |
| EUR | method | Beagle - Eagle | 0 | 0.0004332 | 5.85e-05 | 1194 | 7.4102562 | 0.0000000 | 21 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0004457 | 5.85e-05 | 1194 | -7.6247750 | 0.0000000 | 21 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008789 | 5.85e-05 | 1194 | -15.0350312 | 0.0000000 | 21 |
| SAS | method | Beagle - Eagle | 0 | 0.0006113 | 6.56e-05 | 1194 | 9.3201362 | 0.0000000 | 21 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0006490 | 6.56e-05 | 1194 | -9.8951103 | 0.0000000 | 21 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0012603 | 6.56e-05 | 1194 | -19.2152465 | 0.0000000 | 21 |
| AFR | method | Beagle - Eagle | 0 | 0.0008486 | 4.65e-05 | 1194 | 18.2576111 | 0.0000000 | 22 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0005283 | 4.65e-05 | 1194 | -11.3668957 | 0.0000000 | 22 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0013769 | 4.65e-05 | 1194 | -29.6245069 | 0.0000000 | 22 |
| AMR | method | Beagle - Eagle | 0 | 0.0005098 | 5.63e-05 | 1194 | 9.0551190 | 0.0000000 | 22 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0005420 | 5.63e-05 | 1194 | -9.6277848 | 0.0000000 | 22 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0010518 | 5.63e-05 | 1194 | -18.6829039 | 0.0000000 | 22 |
| EAS | method | Beagle - Eagle | 0 | 0.0005407 | 7.77e-05 | 1194 | 6.9627479 | 0.0000000 | 22 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0005423 | 7.77e-05 | 1194 | -6.9832513 | 0.0000000 | 22 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0010830 | 7.77e-05 | 1194 | -13.9459992 | 0.0000000 | 22 |
| EUR | method | Beagle - Eagle | 0 | 0.0003903 | 6.37e-05 | 1194 | 6.1269545 | 0.0000000 | 22 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0004136 | 6.37e-05 | 1194 | -6.4927862 | 0.0000000 | 22 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0008039 | 6.37e-05 | 1194 | -12.6197407 | 0.0000000 | 22 |
| SAS | method | Beagle - Eagle | 0 | 0.0006218 | 7.15e-05 | 1194 | 8.7001914 | 0.0000000 | 22 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0007412 | 7.15e-05 | 1194 | -10.3710731 | 0.0000000 | 22 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0013631 | 7.15e-05 | 1194 | -19.0712645 | 0.0000000 | 22 |
| AFR | method | Beagle - Eagle | 0 | 0.0000090 | 1.32e-05 | 1990 | 0.6832970 | 0.7732702 | 23 |
| AFR | method | Beagle - SHAPEIT | 0 | -0.0001865 | 1.32e-05 | 1990 | -14.1689679 | 0.0000000 | 23 |
| AFR | method | Eagle - SHAPEIT | 0 | -0.0001955 | 1.32e-05 | 1990 | -14.8522649 | 0.0000000 | 23 |
| AMR | method | Beagle - Eagle | 0 | 0.0000208 | 1.32e-05 | 1990 | 1.5785688 | 0.2551503 | 23 |
| AMR | method | Beagle - SHAPEIT | 0 | -0.0001695 | 1.32e-05 | 1990 | -12.8743522 | 0.0000000 | 23 |
| AMR | method | Eagle - SHAPEIT | 0 | -0.0001902 | 1.32e-05 | 1990 | -14.4529210 | 0.0000000 | 23 |
| EAS | method | Beagle - Eagle | 0 | 0.0000128 | 1.32e-05 | 1990 | 0.9717229 | 0.5948612 | 23 |
| EAS | method | Beagle - SHAPEIT | 0 | -0.0001560 | 1.32e-05 | 1990 | -11.8509140 | 0.0000000 | 23 |
| EAS | method | Eagle - SHAPEIT | 0 | -0.0001688 | 1.32e-05 | 1990 | -12.8226369 | 0.0000000 | 23 |
| EUR | method | Beagle - Eagle | 0 | 0.0000119 | 1.32e-05 | 1990 | 0.9049559 | 0.6372251 | 23 |
| EUR | method | Beagle - SHAPEIT | 0 | -0.0001806 | 1.32e-05 | 1990 | -13.7242659 | 0.0000000 | 23 |
| EUR | method | Eagle - SHAPEIT | 0 | -0.0001925 | 1.32e-05 | 1990 | -14.6292218 | 0.0000000 | 23 |
| SAS | method | Beagle - Eagle | 0 | -0.0000318 | 1.32e-05 | 1990 | -2.4127848 | 0.0420849 | 23 |
| SAS | method | Beagle - SHAPEIT | 0 | -0.0002085 | 1.32e-05 | 1990 | -15.8443297 | 0.0000000 | 23 |
| SAS | method | Eagle - SHAPEIT | 0 | -0.0001768 | 1.32e-05 | 1990 | -13.4315449 | 0.0000000 | 23 |
df_pop_pop %>% knitr::kable()
| method | term | contrast | null.value | estimate | std.error | df | statistic | adj.p.value | chrom |
|---|---|---|---|---|---|---|---|---|---|
| Beagle | SUPER | AFR - AMR | 0 | -0.0007318 | 0.0001295 | 634.6203 | -5.6529163 | 0.0000002 | 1 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0026433 | 0.0001605 | 634.6203 | -16.4701971 | 0.0000000 | 1 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005607 | 0.0001398 | 634.6203 | -4.0098589 | 0.0006479 | 1 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0021981 | 0.0001512 | 634.6203 | -14.5388504 | 0.0000000 | 1 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0019115 | 0.0001701 | 634.6203 | -11.2381013 | 0.0000000 | 1 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001711 | 0.0001508 | 634.6203 | 1.1349456 | 0.7879365 | 1 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0014662 | 0.0001613 | 634.6203 | -9.0878937 | 0.0000000 | 1 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0020826 | 0.0001781 | 634.6203 | 11.6923806 | 0.0000000 | 1 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004453 | 0.0001872 | 634.6203 | 2.3790629 | 0.1223711 | 1 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0016373 | 0.0001698 | 634.6203 | -9.6439472 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0011347 | 0.0001295 | 634.6203 | -8.7646480 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0029467 | 0.0001605 | 634.6203 | -18.3605031 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0010682 | 0.0001398 | 634.6203 | -7.6386069 | 0.0000000 | 1 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0023939 | 0.0001512 | 634.6203 | -15.8340793 | 0.0000000 | 1 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0018120 | 0.0001701 | 634.6203 | -10.6533194 | 0.0000000 | 1 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000665 | 0.0001508 | 634.6203 | 0.4412002 | 0.9921352 | 1 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0012592 | 0.0001613 | 634.6203 | -7.8047376 | 0.0000000 | 1 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0018786 | 0.0001781 | 634.6203 | 10.5467618 | 0.0000000 | 1 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0005528 | 0.0001872 | 634.6203 | 2.9537531 | 0.0268840 | 1 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0013257 | 0.0001698 | 634.6203 | -7.8085548 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0008525 | 0.0001295 | 634.6203 | -6.5851335 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0027171 | 0.0001605 | 634.6203 | -16.9296343 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004786 | 0.0001398 | 634.6203 | -3.4223401 | 0.0059368 | 1 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0024242 | 0.0001512 | 634.6203 | -16.0342603 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0018646 | 0.0001701 | 634.6203 | -10.9620792 | 0.0000000 | 1 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0003739 | 0.0001508 | 634.6203 | 2.4804295 | 0.0963581 | 1 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0015716 | 0.0001613 | 634.6203 | -9.7411719 | 0.0000000 | 1 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0022385 | 0.0001781 | 634.6203 | 12.5676089 | 0.0000000 | 1 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0002929 | 0.0001872 | 634.6203 | 1.5650529 | 0.5204822 | 1 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0019456 | 0.0001698 | 634.6203 | -11.4594888 | 0.0000000 | 1 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0009213 | 0.0001293 | 637.2694 | -7.1226395 | 0.0000000 | 2 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0027566 | 0.0001604 | 637.2694 | -17.1909150 | 0.0000000 | 2 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004559 | 0.0001397 | 637.2694 | -3.2629891 | 0.0101862 | 2 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0022843 | 0.0001511 | 637.2694 | -15.1223637 | 0.0000000 | 2 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0018353 | 0.0001699 | 637.2694 | -10.7995069 | 0.0000000 | 2 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0004654 | 0.0001506 | 637.2694 | 3.0898106 | 0.0177665 | 2 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0013630 | 0.0001612 | 637.2694 | -8.4553700 | 0.0000000 | 2 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0023007 | 0.0001780 | 637.2694 | 12.9281400 | 0.0000000 | 2 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004723 | 0.0001870 | 637.2694 | 2.5257317 | 0.0862447 | 2 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0018284 | 0.0001696 | 637.2694 | -10.7787067 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0012853 | 0.0001293 | 637.2694 | -9.9369481 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0030943 | 0.0001604 | 637.2694 | -19.2970026 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0009408 | 0.0001397 | 637.2694 | -6.7334498 | 0.0000000 | 2 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0024193 | 0.0001511 | 637.2694 | -16.0162249 | 0.0000000 | 2 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0018090 | 0.0001699 | 637.2694 | -10.6447030 | 0.0000000 | 2 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003446 | 0.0001506 | 637.2694 | 2.2874798 | 0.1502244 | 2 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0011340 | 0.0001612 | 637.2694 | -7.0347607 | 0.0000000 | 2 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0021535 | 0.0001780 | 637.2694 | 12.1012202 | 0.0000000 | 2 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0006750 | 0.0001870 | 637.2694 | 3.6096813 | 0.0030410 | 2 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0014786 | 0.0001696 | 637.2694 | -8.7162740 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0009785 | 0.0001293 | 637.2694 | -7.5645959 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0029484 | 0.0001604 | 637.2694 | -18.3871557 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004042 | 0.0001397 | 637.2694 | -2.8930653 | 0.0321198 | 2 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0024738 | 0.0001511 | 637.2694 | -16.3768429 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0019700 | 0.0001699 | 637.2694 | -11.5918520 | 0.0000000 | 2 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0005743 | 0.0001506 | 637.2694 | 3.8124594 | 0.0014166 | 2 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0014953 | 0.0001612 | 637.2694 | -9.2762684 | 0.0000000 | 2 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0025442 | 0.0001780 | 637.2694 | 14.2964339 | 0.0000000 | 2 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004746 | 0.0001870 | 637.2694 | 2.5381662 | 0.0836247 | 2 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0020696 | 0.0001696 | 637.2694 | -12.2004839 | 0.0000000 | 2 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0007966 | 0.0001254 | 635.7836 | -6.3515083 | 0.0000000 | 3 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0026264 | 0.0001555 | 635.7836 | -16.8917081 | 0.0000000 | 3 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005786 | 0.0001355 | 635.7836 | -4.2707710 | 0.0002173 | 3 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0020990 | 0.0001465 | 635.7836 | -14.3307780 | 0.0000000 | 3 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0018298 | 0.0001648 | 635.7836 | -11.1041104 | 0.0000000 | 3 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0002180 | 0.0001461 | 635.7836 | 1.4928364 | 0.5675191 | 3 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0013024 | 0.0001563 | 635.7836 | -8.3323635 | 0.0000000 | 3 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0020478 | 0.0001726 | 635.7836 | 11.8673446 | 0.0000000 | 3 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005274 | 0.0001813 | 635.7836 | 2.9085959 | 0.0307031 | 3 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0015204 | 0.0001645 | 635.7836 | -9.2437650 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0011999 | 0.0001254 | 635.7836 | -9.5666227 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0029595 | 0.0001555 | 635.7836 | -19.0338487 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0011011 | 0.0001355 | 635.7836 | -8.1274319 | 0.0000000 | 3 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0023125 | 0.0001465 | 635.7836 | -15.7885370 | 0.0000000 | 3 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0017596 | 0.0001648 | 635.7836 | -10.6782633 | 0.0000000 | 3 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000988 | 0.0001461 | 635.7836 | 0.6764657 | 0.9614685 | 3 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0011127 | 0.0001563 | 635.7836 | -7.1185536 | 0.0000000 | 3 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0018584 | 0.0001726 | 635.7836 | 10.7697101 | 0.0000000 | 3 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0006469 | 0.0001813 | 635.7836 | 3.5679475 | 0.0035411 | 3 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0012115 | 0.0001645 | 635.7836 | -7.3653855 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0008649 | 0.0001254 | 635.7836 | -6.8958807 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0026849 | 0.0001555 | 635.7836 | -17.2682319 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004916 | 0.0001355 | 635.7836 | -3.6290189 | 0.0028329 | 3 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0022789 | 0.0001465 | 635.7836 | -15.5589179 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0018200 | 0.0001648 | 635.7836 | -11.0450509 | 0.0000000 | 3 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0003732 | 0.0001461 | 635.7836 | 2.5555705 | 0.0800688 | 3 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0014140 | 0.0001563 | 635.7836 | -9.0464011 | 0.0000000 | 3 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0021933 | 0.0001726 | 635.7836 | 12.7104415 | 0.0000000 | 3 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004060 | 0.0001813 | 635.7836 | 2.2393857 | 0.1666180 | 3 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0017873 | 0.0001645 | 635.7836 | -10.8659754 | 0.0000000 | 3 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0009254 | 0.0001150 | 646.7191 | -8.0490906 | 0.0000000 | 4 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0023588 | 0.0001425 | 646.7191 | -16.5501304 | 0.0000000 | 4 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005374 | 0.0001242 | 646.7191 | -4.3278569 | 0.0001692 | 4 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0020837 | 0.0001343 | 646.7191 | -15.5199665 | 0.0000000 | 4 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0014334 | 0.0001511 | 646.7191 | -9.4897459 | 0.0000000 | 4 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003879 | 0.0001339 | 646.7191 | 2.8976528 | 0.0316821 | 4 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0011583 | 0.0001433 | 646.7191 | -8.0845605 | 0.0000000 | 4 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0018214 | 0.0001582 | 646.7191 | 11.5147488 | 0.0000000 | 4 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0002751 | 0.0001662 | 646.7191 | 1.6550659 | 0.4627529 | 4 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0015463 | 0.0001508 | 646.7191 | -10.2557006 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0013097 | 0.0001150 | 646.7191 | -11.3916004 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0027357 | 0.0001425 | 646.7191 | -19.1944371 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0009896 | 0.0001242 | 646.7191 | -7.9687864 | 0.0000000 | 4 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0022520 | 0.0001343 | 646.7191 | -16.7735518 | 0.0000000 | 4 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0014260 | 0.0001511 | 646.7191 | -9.4407604 | 0.0000000 | 4 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003201 | 0.0001339 | 646.7191 | 2.3907847 | 0.1190861 | 4 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0009424 | 0.0001433 | 646.7191 | -6.5772043 | 0.0000000 | 4 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0017461 | 0.0001582 | 646.7191 | 11.0389585 | 0.0000000 | 4 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0004837 | 0.0001662 | 646.7191 | 2.9099644 | 0.0305661 | 4 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0012625 | 0.0001508 | 646.7191 | -8.3731921 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0010420 | 0.0001150 | 646.7191 | -9.0637005 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0025324 | 0.0001425 | 646.7191 | -17.7682398 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004991 | 0.0001242 | 646.7191 | -4.0188066 | 0.0006235 | 4 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0022172 | 0.0001343 | 646.7191 | -16.5138367 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0014904 | 0.0001511 | 646.7191 | -9.8668672 | 0.0000000 | 4 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0005430 | 0.0001339 | 646.7191 | 4.0555932 | 0.0005364 | 4 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0011751 | 0.0001433 | 646.7191 | -8.2017520 | 0.0000000 | 4 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0020334 | 0.0001582 | 646.7191 | 12.8549567 | 0.0000000 | 4 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0003153 | 0.0001662 | 646.7191 | 1.8967721 | 0.3200442 | 4 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0017181 | 0.0001508 | 646.7191 | -11.3952718 | 0.0000000 | 4 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0006740 | 0.0001304 | 637.7817 | -5.1704390 | 0.0000031 | 5 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0025078 | 0.0001616 | 637.7817 | -15.5185523 | 0.0000000 | 5 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004742 | 0.0001408 | 637.7817 | -3.3680775 | 0.0071550 | 5 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0021772 | 0.0001522 | 637.7817 | -14.3018027 | 0.0000000 | 5 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0018338 | 0.0001713 | 637.7817 | -10.7073889 | 0.0000000 | 5 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001998 | 0.0001518 | 637.7817 | 1.3159190 | 0.6814036 | 5 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0015032 | 0.0001625 | 637.7817 | -9.2529070 | 0.0000000 | 5 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0020336 | 0.0001793 | 637.7817 | 11.3387550 | 0.0000000 | 5 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0003306 | 0.0001885 | 637.7817 | 1.7544970 | 0.4013676 | 5 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0017029 | 0.0001710 | 637.7817 | -9.9614553 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0011415 | 0.0001304 | 637.7817 | -8.7568075 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0028415 | 0.0001616 | 637.7817 | -17.5836014 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0009759 | 0.0001408 | 637.7817 | -6.9311149 | 0.0000000 | 5 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0023625 | 0.0001522 | 637.7817 | -15.5191769 | 0.0000000 | 5 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0017000 | 0.0001713 | 637.7817 | -9.9262320 | 0.0000000 | 5 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0001656 | 0.0001518 | 637.7817 | 1.0907097 | 0.8113679 | 5 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0012210 | 0.0001625 | 637.7817 | -7.5159454 | 0.0000000 | 5 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0018656 | 0.0001793 | 637.7817 | 10.4021768 | 0.0000000 | 5 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0004790 | 0.0001885 | 637.7817 | 2.5419231 | 0.0828449 | 5 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0013866 | 0.0001710 | 637.7817 | -8.1108562 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0007978 | 0.0001304 | 637.7817 | -6.1204913 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0026962 | 0.0001616 | 637.7817 | -16.6846301 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003933 | 0.0001408 | 637.7817 | -2.7935710 | 0.0426224 | 5 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0023583 | 0.0001522 | 637.7817 | -15.4915609 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0018984 | 0.0001713 | 637.7817 | -11.0845512 | 0.0000000 | 5 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004045 | 0.0001518 | 637.7817 | 2.6646487 | 0.0604675 | 5 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0015605 | 0.0001625 | 637.7817 | -9.6054592 | 0.0000000 | 5 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0023029 | 0.0001793 | 637.7817 | 12.8404856 | 0.0000000 | 5 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0003380 | 0.0001885 | 637.7817 | 1.7933476 | 0.3783077 | 5 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0019649 | 0.0001710 | 637.7817 | -11.4941014 | 0.0000000 | 5 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0006305 | 0.0001157 | 637.8403 | -5.4492722 | 0.0000007 | 6 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0022255 | 0.0001434 | 637.8403 | -15.5161836 | 0.0000000 | 6 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003023 | 0.0001250 | 637.8403 | -2.4193871 | 0.1114328 | 6 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0018604 | 0.0001351 | 637.8403 | -13.7691065 | 0.0000000 | 6 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0015950 | 0.0001520 | 637.8403 | -10.4929281 | 0.0000000 | 6 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003281 | 0.0001347 | 637.8403 | 2.4353303 | 0.1073266 | 6 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0012299 | 0.0001442 | 637.8403 | -8.5300001 | 0.0000000 | 6 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0019231 | 0.0001592 | 637.8403 | 12.0814238 | 0.0000000 | 6 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0003651 | 0.0001673 | 637.8403 | 2.1827753 | 0.1875155 | 6 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0015580 | 0.0001517 | 637.8403 | -10.2684747 | 0.0000000 | 6 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0010403 | 0.0001157 | 637.8403 | -8.9920646 | 0.0000000 | 6 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0025019 | 0.0001434 | 637.8403 | -17.4437864 | 0.0000000 | 6 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0007401 | 0.0001250 | 637.8403 | -5.9219707 | 0.0000001 | 6 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0020271 | 0.0001351 | 637.8403 | -15.0030516 | 0.0000000 | 6 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0014616 | 0.0001520 | 637.8403 | -9.6152489 | 0.0000000 | 6 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003003 | 0.0001347 | 637.8403 | 2.2287756 | 0.1703975 | 6 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0009867 | 0.0001442 | 637.8403 | -6.8435322 | 0.0000000 | 6 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0017619 | 0.0001592 | 637.8403 | 11.0684612 | 0.0000000 | 6 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0004748 | 0.0001673 | 637.8403 | 2.8389530 | 0.0375143 | 6 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0012870 | 0.0001517 | 637.8403 | -8.4824239 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0006899 | 0.0001157 | 637.8403 | -5.9633534 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0022925 | 0.0001434 | 637.8403 | -15.9836923 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0002138 | 0.0001250 | 637.8403 | -1.7110384 | 0.4278191 | 6 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0019980 | 0.0001351 | 637.8403 | -14.7874880 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0016026 | 0.0001520 | 637.8403 | -10.5427738 | 0.0000000 | 6 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004761 | 0.0001347 | 637.8403 | 3.5338250 | 0.0040039 | 6 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0013080 | 0.0001442 | 637.8403 | -9.0717867 | 0.0000000 | 6 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0020787 | 0.0001592 | 637.8403 | 13.0587868 | 0.0000000 | 6 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0002946 | 0.0001673 | 637.8403 | 1.7610282 | 0.3974503 | 6 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0017841 | 0.0001517 | 637.8403 | -11.7587502 | 0.0000000 | 6 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0007361 | 0.0001246 | 645.0304 | -5.9092743 | 0.0000001 | 7 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0025845 | 0.0001544 | 645.0304 | -16.7364847 | 0.0000000 | 7 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003421 | 0.0001345 | 645.0304 | -2.5422493 | 0.0827634 | 7 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0020941 | 0.0001455 | 645.0304 | -14.3958150 | 0.0000000 | 7 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0018484 | 0.0001637 | 645.0304 | -11.2942408 | 0.0000000 | 7 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003940 | 0.0001451 | 645.0304 | 2.7163864 | 0.0526590 | 7 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0013580 | 0.0001552 | 645.0304 | -8.7481578 | 0.0000000 | 7 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0022424 | 0.0001714 | 645.0304 | 13.0845182 | 0.0000000 | 7 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004903 | 0.0001801 | 645.0304 | 2.7229525 | 0.0517329 | 7 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0017521 | 0.0001634 | 645.0304 | -10.7253549 | 0.0000000 | 7 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0010483 | 0.0001246 | 645.0304 | -8.4161640 | 0.0000000 | 7 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0027912 | 0.0001544 | 645.0304 | -18.0753326 | 0.0000000 | 7 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0007835 | 0.0001345 | 645.0304 | -5.8230836 | 0.0000001 | 7 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0022046 | 0.0001455 | 645.0304 | -15.1551609 | 0.0000000 | 7 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0017429 | 0.0001637 | 645.0304 | -10.6494816 | 0.0000000 | 7 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002649 | 0.0001451 | 645.0304 | 1.8259556 | 0.3594153 | 7 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0011562 | 0.0001552 | 645.0304 | -7.4481734 | 0.0000000 | 7 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0020077 | 0.0001714 | 645.0304 | 11.7151505 | 0.0000000 | 7 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0005866 | 0.0001801 | 645.0304 | 3.2576416 | 0.0103620 | 7 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0014211 | 0.0001634 | 645.0304 | -8.6993220 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0007233 | 0.0001246 | 645.0304 | -5.8069757 | 0.0000001 | 7 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0025946 | 0.0001544 | 645.0304 | -16.8023228 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0002229 | 0.0001345 | 645.0304 | -1.6570107 | 0.4615261 | 7 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0022346 | 0.0001455 | 645.0304 | -15.3613727 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0018713 | 0.0001637 | 645.0304 | -11.4342247 | 0.0000000 | 7 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0005004 | 0.0001451 | 645.0304 | 3.4496526 | 0.0053924 | 7 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0015112 | 0.0001552 | 645.0304 | -9.7350310 | 0.0000000 | 7 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0023717 | 0.0001714 | 645.0304 | 13.8388298 | 0.0000000 | 7 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0003601 | 0.0001801 | 645.0304 | 1.9994366 | 0.2673763 | 7 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0020116 | 0.0001634 | 645.0304 | -12.3142848 | 0.0000000 | 7 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0009059 | 0.0001328 | 652.8377 | -6.8225783 | 0.0000000 | 8 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0028274 | 0.0001646 | 652.8377 | -17.1771221 | 0.0000000 | 8 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005110 | 0.0001434 | 652.8377 | -3.5628465 | 0.0036009 | 8 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0021225 | 0.0001551 | 652.8377 | -13.6883188 | 0.0000000 | 8 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0019215 | 0.0001744 | 652.8377 | -11.0148751 | 0.0000000 | 8 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003949 | 0.0001546 | 652.8377 | 2.5540025 | 0.0803515 | 8 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0012166 | 0.0001655 | 652.8377 | -7.3523501 | 0.0000000 | 8 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0023164 | 0.0001827 | 652.8377 | 12.6802982 | 0.0000000 | 8 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0007049 | 0.0001920 | 652.8377 | 3.6723189 | 0.0024081 | 8 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0016115 | 0.0001741 | 652.8377 | -9.2547385 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0013962 | 0.0001328 | 652.8377 | -10.5155964 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0031391 | 0.0001646 | 652.8377 | -19.0712514 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0010459 | 0.0001434 | 652.8377 | -7.2926473 | 0.0000000 | 8 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0023648 | 0.0001551 | 652.8377 | -15.2511374 | 0.0000000 | 8 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0017429 | 0.0001744 | 652.8377 | -9.9912717 | 0.0000000 | 8 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003503 | 0.0001546 | 652.8377 | 2.2656932 | 0.1574626 | 8 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0009686 | 0.0001655 | 652.8377 | -5.8535156 | 0.0000001 | 8 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0020933 | 0.0001827 | 652.8377 | 11.4587892 | 0.0000000 | 8 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0007744 | 0.0001920 | 652.8377 | 4.0341300 | 0.0005851 | 8 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0013189 | 0.0001741 | 652.8377 | -7.5743995 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0010047 | 0.0001328 | 652.8377 | -7.5671741 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0027687 | 0.0001646 | 652.8377 | -16.8206078 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003785 | 0.0001434 | 652.8377 | -2.6391939 | 0.0646155 | 8 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0022780 | 0.0001551 | 652.8377 | -14.6912134 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0017640 | 0.0001744 | 652.8377 | -10.1117547 | 0.0000000 | 8 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0006262 | 0.0001546 | 652.8377 | 4.0501547 | 0.0005479 | 8 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0012732 | 0.0001655 | 652.8377 | -7.6946586 | 0.0000000 | 8 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0023902 | 0.0001827 | 652.8377 | 13.0842075 | 0.0000000 | 8 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004907 | 0.0001920 | 652.8377 | 2.5564680 | 0.0798559 | 8 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0018995 | 0.0001741 | 652.8377 | -10.9085553 | 0.0000000 | 8 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0005758 | 0.0001327 | 646.2063 | -4.3390163 | 0.0001612 | 9 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0026399 | 0.0001645 | 646.2063 | -16.0458333 | 0.0000000 | 9 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003953 | 0.0001433 | 646.2063 | -2.7573899 | 0.0470956 | 9 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0020545 | 0.0001550 | 646.2063 | -13.2567412 | 0.0000000 | 9 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0020640 | 0.0001744 | 646.2063 | -11.8377240 | 0.0000000 | 9 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001806 | 0.0001545 | 646.2063 | 1.1684006 | 0.7694431 | 9 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0014787 | 0.0001654 | 646.2063 | -8.9407557 | 0.0000000 | 9 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0022446 | 0.0001826 | 646.2063 | 12.2933033 | 0.0000000 | 9 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005853 | 0.0001919 | 646.2063 | 3.0508456 | 0.0200357 | 9 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0016593 | 0.0001740 | 646.2063 | -9.5338297 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0009903 | 0.0001327 | 646.2063 | -7.4620550 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0029117 | 0.0001645 | 646.2063 | -17.6982554 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0008789 | 0.0001433 | 646.2063 | -6.1310076 | 0.0000000 | 9 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0022293 | 0.0001550 | 646.2063 | -14.3846208 | 0.0000000 | 9 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0019214 | 0.0001744 | 646.2063 | -11.0198779 | 0.0000000 | 9 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0001114 | 0.0001545 | 646.2063 | 0.7210139 | 0.9516534 | 9 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0012391 | 0.0001654 | 646.2063 | -7.4917100 | 0.0000000 | 9 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0020329 | 0.0001826 | 646.2063 | 11.1336385 | 0.0000000 | 9 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0006824 | 0.0001919 | 646.2063 | 3.5567302 | 0.0036839 | 9 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0013505 | 0.0001740 | 646.2063 | -7.7595503 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0006411 | 0.0001327 | 646.2063 | -4.8309266 | 0.0000168 | 9 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0026601 | 0.0001645 | 646.2063 | -16.1688267 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0002189 | 0.0001433 | 646.2063 | -1.5268710 | 0.5453062 | 9 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0022083 | 0.0001550 | 646.2063 | -14.2489629 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0020190 | 0.0001744 | 646.2063 | -11.5793729 | 0.0000000 | 9 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004222 | 0.0001545 | 646.2063 | 2.7322012 | 0.0504498 | 9 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0015672 | 0.0001654 | 646.2063 | -9.4758191 | 0.0000000 | 9 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0024412 | 0.0001826 | 646.2063 | 13.3701893 | 0.0000000 | 9 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004518 | 0.0001919 | 646.2063 | 2.3548023 | 0.1293093 | 9 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0019894 | 0.0001740 | 646.2063 | -11.4308893 | 0.0000000 | 9 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0006314 | 0.0001174 | 652.8895 | -5.3760585 | 0.0000011 | 10 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0022866 | 0.0001456 | 652.8895 | -15.7044124 | 0.0000000 | 10 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0002953 | 0.0001269 | 652.8895 | -2.3280256 | 0.1373257 | 10 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0019328 | 0.0001372 | 652.8895 | -14.0921578 | 0.0000000 | 10 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0016552 | 0.0001543 | 652.8895 | -10.7262582 | 0.0000000 | 10 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003361 | 0.0001368 | 652.8895 | 2.4572029 | 0.1018566 | 10 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0013014 | 0.0001464 | 652.8895 | -8.8914666 | 0.0000000 | 10 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0019912 | 0.0001616 | 652.8895 | 12.3227540 | 0.0000000 | 10 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0003537 | 0.0001698 | 652.8895 | 2.0832255 | 0.2285453 | 10 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0016375 | 0.0001540 | 652.8895 | -10.6313957 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0010254 | 0.0001174 | 652.8895 | -8.7305803 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0026105 | 0.0001456 | 652.8895 | -17.9292957 | 0.0000000 | 10 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0007495 | 0.0001269 | 652.8895 | -5.9076566 | 0.0000001 | 10 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0021702 | 0.0001372 | 652.8895 | -15.8223888 | 0.0000000 | 10 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0015851 | 0.0001543 | 652.8895 | -10.2723781 | 0.0000000 | 10 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002759 | 0.0001368 | 652.8895 | 2.0175080 | 0.2586651 | 10 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0011448 | 0.0001464 | 652.8895 | -7.8211189 | 0.0000000 | 10 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0018611 | 0.0001616 | 652.8895 | 11.5171669 | 0.0000000 | 10 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0004403 | 0.0001698 | 652.8895 | 2.5934288 | 0.0727193 | 10 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0014207 | 0.0001540 | 652.8895 | -9.2238204 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0006838 | 0.0001174 | 652.8895 | -5.8223057 | 0.0000001 | 10 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0023877 | 0.0001456 | 652.8895 | -16.3989433 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0001801 | 0.0001269 | 652.8895 | -1.4200295 | 0.6149264 | 10 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0021015 | 0.0001372 | 652.8895 | -15.3214358 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0017039 | 0.0001543 | 652.8895 | -11.0419432 | 0.0000000 | 10 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0005037 | 0.0001368 | 652.8895 | 3.6826315 | 0.0023171 | 10 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0014176 | 0.0001464 | 652.8895 | -9.6853067 | 0.0000000 | 10 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0022075 | 0.0001616 | 652.8895 | 13.6614154 | 0.0000000 | 10 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0002862 | 0.0001698 | 652.8895 | 1.6857926 | 0.4434519 | 10 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0019213 | 0.0001540 | 652.8895 | -12.4739082 | 0.0000000 | 10 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0008881 | 0.0001337 | 645.9162 | -6.6449083 | 0.0000000 | 11 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0025694 | 0.0001657 | 645.9162 | -15.5069028 | 0.0000000 | 11 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004370 | 0.0001444 | 645.9162 | -3.0272624 | 0.0215370 | 11 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0023209 | 0.0001561 | 645.9162 | -14.8694553 | 0.0000000 | 11 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0016813 | 0.0001756 | 645.9162 | -9.5741479 | 0.0000000 | 11 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0004511 | 0.0001556 | 645.9162 | 2.8982188 | 0.0316311 | 11 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0014328 | 0.0001666 | 645.9162 | -8.6017126 | 0.0000000 | 11 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0021323 | 0.0001839 | 645.9162 | 11.5958272 | 0.0000000 | 11 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0002485 | 0.0001932 | 645.9162 | 1.2859601 | 0.6999985 | 11 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0018839 | 0.0001753 | 645.9162 | -10.7476491 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0012623 | 0.0001337 | 645.9162 | -9.4446092 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0028490 | 0.0001657 | 645.9162 | -17.1943653 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0009377 | 0.0001444 | 645.9162 | -6.4952428 | 0.0000000 | 11 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0024816 | 0.0001561 | 645.9162 | -15.8989505 | 0.0000000 | 11 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0015867 | 0.0001756 | 645.9162 | -9.0354637 | 0.0000000 | 11 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003246 | 0.0001556 | 645.9162 | 2.0856446 | 0.2274959 | 11 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0012193 | 0.0001666 | 645.9162 | -7.3199222 | 0.0000000 | 11 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0019113 | 0.0001839 | 645.9162 | 10.3936527 | 0.0000000 | 11 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0003674 | 0.0001932 | 645.9162 | 1.9013670 | 0.3175734 | 11 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0015439 | 0.0001753 | 645.9162 | -8.8080393 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0009258 | 0.0001337 | 645.9162 | -6.9266630 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0026906 | 0.0001657 | 645.9162 | -16.2383552 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003378 | 0.0001444 | 645.9162 | -2.3398088 | 0.1337613 | 11 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0024526 | 0.0001561 | 645.9162 | -15.7131379 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0017648 | 0.0001756 | 645.9162 | -10.0498693 | 0.0000000 | 11 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0005880 | 0.0001556 | 645.9162 | 3.7778259 | 0.0016169 | 11 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0015268 | 0.0001666 | 645.9162 | -9.1662151 | 0.0000000 | 11 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0023528 | 0.0001839 | 645.9162 | 12.7946120 | 0.0000000 | 11 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0002380 | 0.0001932 | 645.9162 | 1.2316703 | 0.7328459 | 11 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0021148 | 0.0001753 | 645.9162 | -12.0651479 | 0.0000000 | 11 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0007627 | 0.0001348 | 646.0960 | -5.6592590 | 0.0000002 | 12 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0025199 | 0.0001671 | 646.0960 | -15.0821499 | 0.0000000 | 12 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004272 | 0.0001456 | 646.0960 | -2.9342325 | 0.0284667 | 12 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0022723 | 0.0001574 | 646.0960 | -14.4372952 | 0.0000000 | 12 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0017572 | 0.0001771 | 646.0960 | -9.9235652 | 0.0000000 | 12 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003356 | 0.0001569 | 646.0960 | 2.1381019 | 0.2052420 | 12 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0015096 | 0.0001680 | 646.0960 | -8.9876408 | 0.0000000 | 12 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0020928 | 0.0001854 | 646.0960 | 11.2861403 | 0.0000000 | 12 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0002476 | 0.0001948 | 646.0960 | 1.2708241 | 0.7092743 | 12 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0018452 | 0.0001768 | 646.0960 | -10.4394404 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0011905 | 0.0001348 | 646.0960 | -8.8332387 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0028558 | 0.0001671 | 646.0960 | -17.0923896 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0009131 | 0.0001456 | 646.0960 | -6.2724569 | 0.0000000 | 12 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0023826 | 0.0001574 | 646.0960 | -15.1378204 | 0.0000000 | 12 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0016653 | 0.0001771 | 646.0960 | -9.4045699 | 0.0000000 | 12 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002774 | 0.0001569 | 646.0960 | 1.7672893 | 0.3936989 | 12 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0011921 | 0.0001680 | 646.0960 | -7.0972617 | 0.0000000 | 12 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0019427 | 0.0001854 | 646.0960 | 10.4766736 | 0.0000000 | 12 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0004732 | 0.0001948 | 646.0960 | 2.4287585 | 0.1089874 | 12 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0014695 | 0.0001768 | 646.0960 | -8.3137598 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0008319 | 0.0001348 | 646.0960 | -6.1723147 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0026273 | 0.0001671 | 646.0960 | -15.7248272 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003731 | 0.0001456 | 646.0960 | -2.5626655 | 0.0786338 | 12 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0025230 | 0.0001574 | 646.0960 | -16.0301577 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0017954 | 0.0001771 | 646.0960 | -10.1394739 | 0.0000000 | 12 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004588 | 0.0001569 | 646.0960 | 2.9233301 | 0.0293942 | 12 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0016912 | 0.0001680 | 646.0960 | -10.0685750 | 0.0000000 | 12 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0022543 | 0.0001854 | 646.0960 | 12.1569363 | 0.0000000 | 12 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0001043 | 0.0001948 | 646.0960 | 0.5352240 | 0.9836739 | 12 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0021500 | 0.0001768 | 646.0960 | -12.1638958 | 0.0000000 | 12 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0006153 | 0.0001289 | 669.0456 | -4.7743042 | 0.0000218 | 13 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0023526 | 0.0001598 | 669.0456 | -14.7259570 | 0.0000000 | 13 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004368 | 0.0001392 | 669.0456 | -3.1382968 | 0.0152258 | 13 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0018945 | 0.0001505 | 669.0456 | -12.5885369 | 0.0000000 | 13 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0017373 | 0.0001693 | 669.0456 | -10.2610323 | 0.0000000 | 13 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001784 | 0.0001501 | 669.0456 | 1.1888814 | 0.7578176 | 13 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0012793 | 0.0001606 | 669.0456 | -7.9653293 | 0.0000000 | 13 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0019158 | 0.0001773 | 669.0456 | 10.8049849 | 0.0000000 | 13 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004581 | 0.0001863 | 669.0456 | 2.4588011 | 0.1014366 | 13 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0014577 | 0.0001690 | 669.0456 | -8.6250750 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0009492 | 0.0001289 | 669.0456 | -7.3652891 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0027004 | 0.0001598 | 669.0456 | -16.9026822 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0008758 | 0.0001392 | 669.0456 | -6.2916039 | 0.0000000 | 13 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0022733 | 0.0001505 | 669.0456 | -15.1057387 | 0.0000000 | 13 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0017512 | 0.0001693 | 669.0456 | -10.3428558 | 0.0000000 | 13 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000734 | 0.0001501 | 669.0456 | 0.4889550 | 0.9883788 | 13 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0013242 | 0.0001606 | 669.0456 | -8.2450884 | 0.0000000 | 13 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0018246 | 0.0001773 | 669.0456 | 10.2907058 | 0.0000000 | 13 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0004270 | 0.0001863 | 669.0456 | 2.2919966 | 0.1486828 | 13 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0013976 | 0.0001690 | 669.0456 | -8.2694214 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0006906 | 0.0001289 | 669.0456 | -5.3591698 | 0.0000011 | 13 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0024239 | 0.0001598 | 669.0456 | -15.1724421 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003240 | 0.0001392 | 669.0456 | -2.3274686 | 0.1374642 | 13 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0021408 | 0.0001505 | 669.0456 | -14.2250141 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0017333 | 0.0001693 | 669.0456 | -10.2371656 | 0.0000000 | 13 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0003667 | 0.0001501 | 669.0456 | 2.4432167 | 0.1052775 | 13 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0014502 | 0.0001606 | 669.0456 | -9.0295128 | 0.0000000 | 13 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0021000 | 0.0001773 | 669.0456 | 11.8438597 | 0.0000000 | 13 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0002831 | 0.0001863 | 669.0456 | 1.5197310 | 0.5499473 | 13 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0018168 | 0.0001690 | 669.0456 | -10.7501608 | 0.0000000 | 13 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0009420 | 0.0001331 | 658.3266 | -7.0779502 | 0.0000000 | 14 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0023472 | 0.0001650 | 658.3266 | -14.2257571 | 0.0000000 | 14 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003467 | 0.0001438 | 658.3266 | -2.4118908 | 0.1133633 | 14 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0021230 | 0.0001554 | 658.3266 | -13.6587651 | 0.0000000 | 14 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0014052 | 0.0001749 | 658.3266 | -8.0357105 | 0.0000000 | 14 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0005953 | 0.0001550 | 658.3266 | 3.8408804 | 0.0012650 | 14 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0011809 | 0.0001659 | 658.3266 | -7.1197449 | 0.0000000 | 14 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0020005 | 0.0001831 | 658.3266 | 10.9245709 | 0.0000000 | 14 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0002242 | 0.0001924 | 658.3266 | 1.1653455 | 0.7711588 | 14 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0017762 | 0.0001745 | 658.3266 | -10.1763917 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0012602 | 0.0001331 | 658.3266 | -9.4686260 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0027527 | 0.0001650 | 658.3266 | -16.6832941 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0008655 | 0.0001438 | 658.3266 | -6.0206863 | 0.0000000 | 14 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0022924 | 0.0001554 | 658.3266 | -14.7491179 | 0.0000000 | 14 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0014925 | 0.0001749 | 658.3266 | -8.5349566 | 0.0000000 | 14 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003947 | 0.0001550 | 658.3266 | 2.5464490 | 0.0818751 | 14 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010322 | 0.0001659 | 658.3266 | -6.2231854 | 0.0000000 | 14 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0018871 | 0.0001831 | 658.3266 | 10.3057198 | 0.0000000 | 14 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0004602 | 0.0001924 | 658.3266 | 2.3919441 | 0.1187438 | 14 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0014269 | 0.0001745 | 658.3266 | -8.1749940 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0009985 | 0.0001331 | 658.3266 | -7.5024312 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0024804 | 0.0001650 | 658.3266 | -15.0332256 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003192 | 0.0001438 | 658.3266 | -2.2204313 | 0.1733737 | 14 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0023074 | 0.0001554 | 658.3266 | -14.8453584 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0014819 | 0.0001749 | 658.3266 | -8.4745259 | 0.0000000 | 14 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0006793 | 0.0001550 | 658.3266 | 4.3829860 | 0.0001325 | 14 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0013089 | 0.0001659 | 658.3266 | -7.8910521 | 0.0000000 | 14 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0021612 | 0.0001831 | 658.3266 | 11.8024521 | 0.0000000 | 14 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0001730 | 0.0001924 | 658.3266 | 0.8992391 | 0.8971656 | 14 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0019882 | 0.0001745 | 658.3266 | -11.3907276 | 0.0000000 | 14 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0006261 | 0.0001426 | 654.9650 | -4.3896754 | 0.0001287 | 15 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0025961 | 0.0001768 | 654.9650 | -14.6832093 | 0.0000000 | 15 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005065 | 0.0001541 | 654.9650 | -3.2879788 | 0.0093636 | 15 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0021253 | 0.0001666 | 654.9650 | -12.7604077 | 0.0000000 | 15 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0019700 | 0.0001874 | 654.9650 | -10.5134461 | 0.0000000 | 15 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0001195 | 0.0001661 | 654.9650 | 0.7197493 | 0.9519534 | 15 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0014992 | 0.0001777 | 654.9650 | -8.4350110 | 0.0000000 | 15 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0020896 | 0.0001962 | 654.9650 | 10.6489538 | 0.0000000 | 15 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004708 | 0.0002062 | 654.9650 | 2.2833077 | 0.1515599 | 15 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0016188 | 0.0001870 | 654.9650 | -8.6548396 | 0.0000000 | 15 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0009513 | 0.0001426 | 654.9650 | -6.6701033 | 0.0000000 | 15 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0028416 | 0.0001768 | 654.9650 | -16.0718895 | 0.0000000 | 15 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0009448 | 0.0001541 | 654.9650 | -6.1329436 | 0.0000000 | 15 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0023409 | 0.0001666 | 654.9650 | -14.0550598 | 0.0000000 | 15 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0018903 | 0.0001874 | 654.9650 | -10.0880715 | 0.0000000 | 15 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0000065 | 0.0001661 | 654.9650 | 0.0391443 | 0.9999995 | 15 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0013896 | 0.0001777 | 654.9650 | -7.8183562 | 0.0000000 | 15 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0018968 | 0.0001962 | 654.9650 | 9.6666823 | 0.0000000 | 15 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0005007 | 0.0002062 | 654.9650 | 2.4283110 | 0.1090845 | 15 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0013961 | 0.0001870 | 654.9650 | -7.4644868 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0007169 | 0.0001426 | 654.9650 | -5.0267370 | 0.0000064 | 15 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0027182 | 0.0001768 | 654.9650 | -15.3741071 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004102 | 0.0001541 | 654.9650 | -2.6625197 | 0.0607778 | 15 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0023991 | 0.0001666 | 654.9650 | -14.4043760 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0020013 | 0.0001874 | 654.9650 | -10.6804703 | 0.0000000 | 15 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0003067 | 0.0001661 | 654.9650 | 1.8469658 | 0.3474785 | 15 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0016822 | 0.0001777 | 654.9650 | -9.4643318 | 0.0000000 | 15 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0023081 | 0.0001962 | 654.9650 | 11.7625260 | 0.0000000 | 15 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0003191 | 0.0002062 | 654.9650 | 1.5477744 | 0.5316887 | 15 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0019889 | 0.0001870 | 654.9650 | -10.6339192 | 0.0000000 | 15 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0008256 | 0.0001565 | 664.8536 | -5.2768148 | 0.0000018 | 16 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0029272 | 0.0001940 | 664.8536 | -15.0908585 | 0.0000000 | 16 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0003634 | 0.0001690 | 664.8536 | -2.1499089 | 0.2004070 | 16 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0024435 | 0.0001827 | 664.8536 | -13.3728041 | 0.0000000 | 16 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0021016 | 0.0002056 | 664.8536 | -10.2228684 | 0.0000000 | 16 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0004623 | 0.0001822 | 664.8536 | 2.5371935 | 0.0837747 | 16 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0016179 | 0.0001950 | 664.8536 | -8.2970204 | 0.0000000 | 16 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0025639 | 0.0002153 | 664.8536 | 11.9097484 | 0.0000000 | 16 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0004837 | 0.0002262 | 664.8536 | 2.1381830 | 0.2051714 | 16 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0020802 | 0.0002052 | 664.8536 | -10.1375261 | 0.0000000 | 16 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0011030 | 0.0001565 | 664.8536 | -7.0493982 | 0.0000000 | 16 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0030829 | 0.0001940 | 664.8536 | -15.8933189 | 0.0000000 | 16 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0009101 | 0.0001690 | 664.8536 | -5.3851443 | 0.0000010 | 16 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0023353 | 0.0001827 | 664.8536 | -12.7805433 | 0.0000000 | 16 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0019799 | 0.0002056 | 664.8536 | -9.6308900 | 0.0000000 | 16 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0001929 | 0.0001822 | 664.8536 | 1.0584865 | 0.8276504 | 16 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0012323 | 0.0001950 | 664.8536 | -6.3197060 | 0.0000000 | 16 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0021727 | 0.0002153 | 664.8536 | 10.0928679 | 0.0000000 | 16 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0007475 | 0.0002262 | 664.8536 | 3.3047323 | 0.0088475 | 16 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0014252 | 0.0002052 | 664.8536 | -6.9454656 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0009145 | 0.0001565 | 664.8536 | -5.8446828 | 0.0000001 | 16 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0029446 | 0.0001940 | 664.8536 | -15.1804752 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004172 | 0.0001690 | 664.8536 | -2.4684448 | 0.0991237 | 16 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0025304 | 0.0001827 | 664.8536 | -13.8481551 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0020301 | 0.0002056 | 664.8536 | -9.8752113 | 0.0000000 | 16 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004973 | 0.0001822 | 664.8536 | 2.7293778 | 0.0508084 | 16 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0016159 | 0.0001950 | 664.8536 | -8.2867944 | 0.0000000 | 16 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0025274 | 0.0002153 | 664.8536 | 11.7404194 | 0.0000000 | 16 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004142 | 0.0002262 | 664.8536 | 1.8310444 | 0.3564806 | 16 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0021132 | 0.0002052 | 664.8536 | -10.2984605 | 0.0000000 | 16 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0007964 | 0.0001560 | 658.8141 | -5.1066707 | 0.0000043 | 17 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0030315 | 0.0001933 | 658.8141 | -15.6799025 | 0.0000000 | 17 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004975 | 0.0001685 | 658.8141 | -2.9532303 | 0.0268961 | 17 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0023810 | 0.0001821 | 658.8141 | -13.0732794 | 0.0000000 | 17 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0022351 | 0.0002049 | 658.8141 | -10.9081681 | 0.0000000 | 17 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0002989 | 0.0001816 | 658.8141 | 1.6459554 | 0.4685086 | 17 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0015846 | 0.0001944 | 658.8141 | -8.1528713 | 0.0000000 | 17 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0025340 | 0.0002146 | 658.8141 | 11.8098300 | 0.0000000 | 17 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0006505 | 0.0002255 | 658.8141 | 2.8852531 | 0.0328256 | 17 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0018835 | 0.0002045 | 658.8141 | -9.2091583 | 0.0000000 | 17 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0010447 | 0.0001560 | 658.8141 | -6.6985295 | 0.0000000 | 17 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0031568 | 0.0001933 | 658.8141 | -16.3280326 | 0.0000000 | 17 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0008668 | 0.0001685 | 658.8141 | -5.1453290 | 0.0000035 | 17 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0024999 | 0.0001821 | 658.8141 | -13.7261569 | 0.0000000 | 17 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0021121 | 0.0002049 | 658.8141 | -10.3081226 | 0.0000000 | 17 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0001779 | 0.0001816 | 658.8141 | 0.9796281 | 0.8644404 | 17 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0014552 | 0.0001944 | 658.8141 | -7.4873441 | 0.0000000 | 17 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0022900 | 0.0002146 | 658.8141 | 10.6728420 | 0.0000000 | 17 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0006569 | 0.0002255 | 658.8141 | 2.9136444 | 0.0302238 | 17 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0016331 | 0.0002045 | 658.8141 | -7.9850405 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0007836 | 0.0001560 | 658.8141 | -5.0243014 | 0.0000065 | 17 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0029472 | 0.0001933 | 658.8141 | -15.2440201 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003464 | 0.0001685 | 658.8141 | -2.0562725 | 0.2405994 | 17 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0025388 | 0.0001821 | 658.8141 | -13.9395701 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0021637 | 0.0002049 | 658.8141 | -10.5595790 | 0.0000000 | 17 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004372 | 0.0001816 | 658.8141 | 2.4072057 | 0.1146088 | 17 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0017552 | 0.0001944 | 658.8141 | -9.0307337 | 0.0000000 | 17 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0026008 | 0.0002146 | 658.8141 | 12.1212671 | 0.0000000 | 17 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0004085 | 0.0002255 | 658.8141 | 1.8116907 | 0.3676003 | 17 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0021924 | 0.0002045 | 658.8141 | -10.7193448 | 0.0000000 | 17 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0009327 | 0.0001291 | 664.4911 | -7.2225102 | 0.0000000 | 18 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0026788 | 0.0001601 | 664.4911 | -16.7334623 | 0.0000000 | 18 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0005296 | 0.0001395 | 664.4911 | -3.7969750 | 0.0014986 | 18 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0021673 | 0.0001508 | 664.4911 | -14.3715377 | 0.0000000 | 18 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0017462 | 0.0001697 | 664.4911 | -10.2918582 | 0.0000000 | 18 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0004031 | 0.0001504 | 664.4911 | 2.6802679 | 0.0579732 | 18 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0012346 | 0.0001609 | 664.4911 | -7.6716621 | 0.0000000 | 18 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0021492 | 0.0001777 | 664.4911 | 12.0967277 | 0.0000000 | 18 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005115 | 0.0001867 | 664.4911 | 2.7399718 | 0.0493654 | 18 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0016377 | 0.0001694 | 664.4911 | -9.6702971 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0012486 | 0.0001291 | 664.4911 | -9.6685518 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0029528 | 0.0001601 | 664.4911 | -18.4444619 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0009995 | 0.0001395 | 664.4911 | -7.1653340 | 0.0000000 | 18 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0022907 | 0.0001508 | 664.4911 | -15.1898541 | 0.0000000 | 18 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0017042 | 0.0001697 | 664.4911 | -10.0445600 | 0.0000000 | 18 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002491 | 0.0001504 | 664.4911 | 1.6564004 | 0.4618919 | 18 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010422 | 0.0001609 | 664.4911 | -6.4757617 | 0.0000000 | 18 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0019533 | 0.0001777 | 664.4911 | 10.9939727 | 0.0000000 | 18 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0006620 | 0.0001867 | 664.4911 | 3.5461514 | 0.0038204 | 18 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0012913 | 0.0001694 | 664.4911 | -7.6246878 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0009898 | 0.0001291 | 664.4911 | -7.6649213 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0026590 | 0.0001601 | 664.4911 | -16.6092307 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003802 | 0.0001395 | 664.4911 | -2.7257526 | 0.0513110 | 18 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0022900 | 0.0001508 | 664.4911 | -15.1850913 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0016691 | 0.0001697 | 664.4911 | -9.8379098 | 0.0000000 | 18 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0006096 | 0.0001504 | 664.4911 | 4.0538048 | 0.0005388 | 18 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0013002 | 0.0001609 | 664.4911 | -8.0790205 | 0.0000000 | 18 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0022788 | 0.0001777 | 664.4911 | 12.8257903 | 0.0000000 | 18 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0003689 | 0.0001867 | 664.4911 | 1.9762561 | 0.2787537 | 18 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0019098 | 0.0001694 | 664.4911 | -11.2770529 | 0.0000000 | 18 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0007560 | 0.0001427 | 670.7882 | -5.2963722 | 0.0000016 | 19 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0026431 | 0.0001770 | 670.7882 | -14.9366944 | 0.0000000 | 19 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004454 | 0.0001542 | 670.7882 | -2.8886689 | 0.0324874 | 19 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0020292 | 0.0001667 | 670.7882 | -12.1733821 | 0.0000000 | 19 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0018871 | 0.0001875 | 670.7882 | -10.0625194 | 0.0000000 | 19 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003106 | 0.0001662 | 670.7882 | 1.8687427 | 0.3353092 | 19 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0012732 | 0.0001779 | 670.7882 | -7.1573935 | 0.0000000 | 19 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0021978 | 0.0001964 | 670.7882 | 11.1908489 | 0.0000000 | 19 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0006139 | 0.0002064 | 670.7882 | 2.9748722 | 0.0252022 | 19 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0015839 | 0.0001872 | 670.7882 | -8.4609891 | 0.0000000 | 19 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0011415 | 0.0001427 | 670.7882 | -7.9966881 | 0.0000000 | 19 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0028256 | 0.0001770 | 670.7882 | -15.9678166 | 0.0000000 | 19 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0008699 | 0.0001542 | 670.7882 | -5.6419124 | 0.0000002 | 19 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0021593 | 0.0001667 | 670.7882 | -12.9535031 | 0.0000000 | 19 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0016841 | 0.0001875 | 670.7882 | -8.9801814 | 0.0000000 | 19 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0002716 | 0.0001662 | 670.7882 | 1.6337859 | 0.4762326 | 19 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0010178 | 0.0001779 | 670.7882 | -5.7216707 | 0.0000002 | 19 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0019557 | 0.0001964 | 670.7882 | 9.9584091 | 0.0000000 | 19 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0006663 | 0.0002064 | 670.7882 | 3.2288992 | 0.0113691 | 19 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0012894 | 0.0001872 | 670.7882 | -6.8879997 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0008285 | 0.0001427 | 670.7882 | -5.8045254 | 0.0000001 | 19 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0027275 | 0.0001770 | 670.7882 | -15.4133644 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0003478 | 0.0001542 | 670.7882 | -2.2557195 | 0.1608399 | 19 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0022152 | 0.0001667 | 670.7882 | -13.2889796 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0018989 | 0.0001875 | 670.7882 | -10.1255213 | 0.0000000 | 19 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004808 | 0.0001662 | 670.7882 | 2.8922091 | 0.0321557 | 19 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0013867 | 0.0001779 | 670.7882 | -7.7950342 | 0.0000000 | 19 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0023797 | 0.0001964 | 670.7882 | 12.1172717 | 0.0000000 | 19 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0005123 | 0.0002064 | 670.7882 | 2.4824504 | 0.0958170 | 19 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0018674 | 0.0001872 | 670.7882 | -9.9757321 | 0.0000000 | 19 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0010025 | 0.0001552 | 658.4350 | -6.4607980 | 0.0000000 | 20 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0029490 | 0.0001924 | 658.4350 | -15.3304764 | 0.0000000 | 20 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0004579 | 0.0001676 | 658.4350 | -2.7318575 | 0.0504773 | 20 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0023596 | 0.0001812 | 658.4350 | -13.0215001 | 0.0000000 | 20 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0019465 | 0.0002039 | 658.4350 | -9.5478089 | 0.0000000 | 20 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0005446 | 0.0001807 | 658.4350 | 3.0141238 | 0.0224018 | 20 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0013571 | 0.0001934 | 658.4350 | -7.0177931 | 0.0000000 | 20 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0024911 | 0.0002135 | 658.4350 | 11.6687765 | 0.0000000 | 20 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0005894 | 0.0002243 | 658.4350 | 2.6274413 | 0.0666120 | 20 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0019017 | 0.0002035 | 658.4350 | -9.3453807 | 0.0000000 | 20 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0013225 | 0.0001552 | 658.4350 | -8.5231533 | 0.0000000 | 20 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0032978 | 0.0001924 | 658.4350 | -17.1435811 | 0.0000000 | 20 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0010072 | 0.0001676 | 658.4350 | -6.0094283 | 0.0000000 | 20 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0025136 | 0.0001812 | 658.4350 | -13.8713466 | 0.0000000 | 20 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0019752 | 0.0002039 | 658.4350 | -9.6888847 | 0.0000000 | 20 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003153 | 0.0001807 | 658.4350 | 1.7449844 | 0.4070748 | 20 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0011911 | 0.0001934 | 658.4350 | -6.1593099 | 0.0000000 | 20 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0022906 | 0.0002135 | 658.4350 | 10.7292997 | 0.0000000 | 20 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0007842 | 0.0002243 | 658.4350 | 3.4957079 | 0.0045785 | 20 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0015064 | 0.0002035 | 658.4350 | -7.4026250 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0011291 | 0.0001552 | 658.4350 | -7.2766280 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0031237 | 0.0001924 | 658.4350 | -16.2387427 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0004334 | 0.0001676 | 658.4350 | -2.5856776 | 0.0741610 | 20 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0025271 | 0.0001812 | 658.4350 | -13.9461593 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0019946 | 0.0002039 | 658.4350 | -9.7838695 | 0.0000000 | 20 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0006957 | 0.0001807 | 658.4350 | 3.8502933 | 0.0012193 | 20 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0013981 | 0.0001934 | 658.4350 | -7.2296315 | 0.0000000 | 20 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0026903 | 0.0002135 | 658.4350 | 12.6019331 | 0.0000000 | 20 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0005966 | 0.0002243 | 658.4350 | 2.6593599 | 0.0612799 | 20 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0020938 | 0.0002035 | 658.4350 | -10.2891744 | 0.0000000 | 20 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0005208 | 0.0001435 | 692.0974 | -3.6295654 | 0.0028108 | 21 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0020027 | 0.0001779 | 692.0974 | -11.2579978 | 0.0000000 | 21 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0002092 | 0.0001550 | 692.0974 | -1.3497751 | 0.6600462 | 21 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0016937 | 0.0001676 | 692.0974 | -10.1071134 | 0.0000000 | 21 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0014819 | 0.0001885 | 692.0974 | -7.8600821 | 0.0000000 | 21 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0003116 | 0.0001671 | 692.0974 | 1.8648221 | 0.3374491 | 21 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0011729 | 0.0001788 | 692.0974 | -6.5586227 | 0.0000000 | 21 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0017935 | 0.0001974 | 692.0974 | 9.0843246 | 0.0000000 | 21 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0003090 | 0.0002074 | 692.0974 | 1.4894484 | 0.5697001 | 21 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0014845 | 0.0001882 | 692.0974 | -7.8885002 | 0.0000000 | 21 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0009006 | 0.0001435 | 692.0974 | -6.2764647 | 0.0000000 | 21 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0021879 | 0.0001779 | 692.0974 | -12.2993288 | 0.0000000 | 21 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0005696 | 0.0001550 | 692.0974 | -3.6751158 | 0.0023733 | 21 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0018760 | 0.0001676 | 692.0974 | -11.1950386 | 0.0000000 | 21 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0012873 | 0.0001885 | 692.0974 | -6.8280330 | 0.0000000 | 21 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003310 | 0.0001671 | 692.0974 | 1.9809010 | 0.2763978 | 21 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0009754 | 0.0001788 | 692.0974 | -5.4541934 | 0.0000007 | 21 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0016183 | 0.0001974 | 692.0974 | 8.1970237 | 0.0000000 | 21 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0003119 | 0.0002074 | 692.0974 | 1.5035868 | 0.5604695 | 21 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0013064 | 0.0001882 | 692.0974 | -6.9420424 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0005376 | 0.0001435 | 692.0974 | -3.7467632 | 0.0018110 | 21 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0019671 | 0.0001779 | 692.0974 | -11.0577831 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0001291 | 0.0001550 | 692.0974 | -0.8328976 | 0.9203687 | 21 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0018169 | 0.0001676 | 692.0974 | -10.8421074 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0014294 | 0.0001885 | 692.0974 | -7.5819655 | 0.0000000 | 21 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0004085 | 0.0001671 | 692.0974 | 2.4448991 | 0.1048151 | 21 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0012792 | 0.0001788 | 692.0974 | -7.1533183 | 0.0000000 | 21 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0018380 | 0.0001974 | 692.0974 | 9.3097144 | 0.0000000 | 21 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0001502 | 0.0002074 | 692.0974 | 0.7240361 | 0.9509401 | 21 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0016878 | 0.0001882 | 692.0974 | -8.9687205 | 0.0000000 | 21 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0006224 | 0.0001654 | 681.1347 | -3.7627727 | 0.0017057 | 22 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0023871 | 0.0002051 | 681.1347 | -11.6403070 | 0.0000000 | 22 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0001454 | 0.0001787 | 681.1347 | -0.8136906 | 0.9264331 | 22 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0020017 | 0.0001932 | 681.1347 | -10.3618521 | 0.0000000 | 22 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0017647 | 0.0002173 | 681.1347 | -8.1194277 | 0.0000000 | 22 |
| Beagle | SUPER | AMR - EUR | 0 | 0.0004771 | 0.0001926 | 681.1347 | 2.4764627 | 0.0971961 | 22 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0013793 | 0.0002062 | 681.1347 | -6.6904427 | 0.0000000 | 22 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0022417 | 0.0002276 | 681.1347 | 9.8496764 | 0.0000000 | 22 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0003854 | 0.0002391 | 681.1347 | 1.6115084 | 0.4904665 | 22 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0018563 | 0.0002169 | 681.1347 | -8.5568803 | 0.0000000 | 22 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0009613 | 0.0001654 | 681.1347 | -5.8108932 | 0.0000001 | 22 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0026950 | 0.0002051 | 681.1347 | -13.1415978 | 0.0000000 | 22 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0006037 | 0.0001787 | 681.1347 | -3.3784911 | 0.0068813 | 22 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0022285 | 0.0001932 | 681.1347 | -11.5356567 | 0.0000000 | 22 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0017338 | 0.0002173 | 681.1347 | -7.9771222 | 0.0000000 | 22 |
| Eagle | SUPER | AMR - EUR | 0 | 0.0003576 | 0.0001926 | 681.1347 | 1.8562377 | 0.3422421 | 22 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0012672 | 0.0002062 | 681.1347 | -6.1469507 | 0.0000000 | 22 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0020913 | 0.0002276 | 681.1347 | 9.1888256 | 0.0000000 | 22 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0004665 | 0.0002391 | 681.1347 | 1.9506974 | 0.2916399 | 22 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0016248 | 0.0002169 | 681.1347 | -7.4896687 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0006362 | 0.0001654 | 681.1347 | -3.8456205 | 0.0012382 | 22 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0024011 | 0.0002051 | 681.1347 | -11.7085075 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0000307 | 0.0001787 | 681.1347 | -0.1717224 | 0.9998051 | 22 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0022147 | 0.0001932 | 681.1347 | -11.4640855 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0017650 | 0.0002173 | 681.1347 | -8.1207219 | 0.0000000 | 22 |
| SHAPEIT | SUPER | AMR - EUR | 0 | 0.0006055 | 0.0001926 | 681.1347 | 3.1430717 | 0.0149867 | 22 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0015785 | 0.0002062 | 681.1347 | -7.6568274 | 0.0000000 | 22 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0023704 | 0.0002276 | 681.1347 | 10.4151285 | 0.0000000 | 22 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0001864 | 0.0002391 | 681.1347 | 0.7796125 | 0.9364814 | 22 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0021840 | 0.0002169 | 681.1347 | -10.0671510 | 0.0000000 | 22 |
| Beagle | SUPER | AFR - AMR | 0 | -0.0000929 | 0.0000362 | 1191.1198 | -2.5662199 | 0.0773715 | 23 |
| Beagle | SUPER | AFR - EAS | 0 | -0.0009474 | 0.0000362 | 1191.1198 | -26.1746698 | 0.0000000 | 23 |
| Beagle | SUPER | AFR - EUR | 0 | -0.0002343 | 0.0000362 | 1191.1198 | -6.4729229 | 0.0000000 | 23 |
| Beagle | SUPER | AFR - SAS | 0 | -0.0005822 | 0.0000362 | 1191.1198 | -16.0858537 | 0.0000000 | 23 |
| Beagle | SUPER | AMR - EAS | 0 | -0.0008545 | 0.0000362 | 1191.1198 | -23.6084499 | 0.0000000 | 23 |
| Beagle | SUPER | AMR - EUR | 0 | -0.0001414 | 0.0000362 | 1191.1198 | -3.9067030 | 0.0009367 | 23 |
| Beagle | SUPER | AMR - SAS | 0 | -0.0004893 | 0.0000362 | 1191.1198 | -13.5196338 | 0.0000000 | 23 |
| Beagle | SUPER | EAS - EUR | 0 | 0.0007131 | 0.0000362 | 1191.1198 | 19.7017469 | 0.0000000 | 23 |
| Beagle | SUPER | EAS - SAS | 0 | 0.0003652 | 0.0000362 | 1191.1198 | 10.0888161 | 0.0000000 | 23 |
| Beagle | SUPER | EUR - SAS | 0 | -0.0003479 | 0.0000362 | 1191.1198 | -9.6129308 | 0.0000000 | 23 |
| Eagle | SUPER | AFR - AMR | 0 | -0.0000811 | 0.0000362 | 1191.1198 | -2.2406667 | 0.1655198 | 23 |
| Eagle | SUPER | AFR - EAS | 0 | -0.0009436 | 0.0000362 | 1191.1198 | -26.0697877 | 0.0000000 | 23 |
| Eagle | SUPER | AFR - EUR | 0 | -0.0002314 | 0.0000362 | 1191.1198 | -6.3923197 | 0.0000000 | 23 |
| Eagle | SUPER | AFR - SAS | 0 | -0.0006230 | 0.0000362 | 1191.1198 | -17.2117010 | 0.0000000 | 23 |
| Eagle | SUPER | AMR - EAS | 0 | -0.0008625 | 0.0000362 | 1191.1198 | -23.8291210 | 0.0000000 | 23 |
| Eagle | SUPER | AMR - EUR | 0 | -0.0001503 | 0.0000362 | 1191.1198 | -4.1516530 | 0.0003406 | 23 |
| Eagle | SUPER | AMR - SAS | 0 | -0.0005419 | 0.0000362 | 1191.1198 | -14.9710343 | 0.0000000 | 23 |
| Eagle | SUPER | EAS - EUR | 0 | 0.0007122 | 0.0000362 | 1191.1198 | 19.6774680 | 0.0000000 | 23 |
| Eagle | SUPER | EAS - SAS | 0 | 0.0003206 | 0.0000362 | 1191.1198 | 8.8580867 | 0.0000000 | 23 |
| Eagle | SUPER | EUR - SAS | 0 | -0.0003916 | 0.0000362 | 1191.1198 | -10.8193813 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AFR - AMR | 0 | -0.0000758 | 0.0000362 | 1191.1198 | -2.0954508 | 0.2226251 | 23 |
| SHAPEIT | SUPER | AFR - EAS | 0 | -0.0009169 | 0.0000362 | 1191.1198 | -25.3317416 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AFR - EUR | 0 | -0.0002284 | 0.0000362 | 1191.1198 | -6.3112132 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AFR - SAS | 0 | -0.0006043 | 0.0000362 | 1191.1198 | -16.6950759 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AMR - EAS | 0 | -0.0008410 | 0.0000362 | 1191.1198 | -23.2362908 | 0.0000000 | 23 |
| SHAPEIT | SUPER | AMR - EUR | 0 | -0.0001526 | 0.0000362 | 1191.1198 | -4.2157624 | 0.0002588 | 23 |
| SHAPEIT | SUPER | AMR - SAS | 0 | -0.0005284 | 0.0000362 | 1191.1198 | -14.5996251 | 0.0000000 | 23 |
| SHAPEIT | SUPER | EAS - EUR | 0 | 0.0006885 | 0.0000362 | 1191.1198 | 19.0205284 | 0.0000000 | 23 |
| SHAPEIT | SUPER | EAS - SAS | 0 | 0.0003126 | 0.0000362 | 1191.1198 | 8.6366657 | 0.0000000 | 23 |
| SHAPEIT | SUPER | EUR - SAS | 0 | -0.0003758 | 0.0000362 | 1191.1198 | -10.3838627 | 0.0000000 | 23 |
cross_meth_plot <- function(df, p_title, p_func, pop, chrom=as.character(chrom)) {
p1 <- p_func(df, "Beagle", "SHAPEIT", pop, chrom = chrom)
p_legend <- cowplot::get_legend(p1)
p1 <- p1 + guides(colour="none") + ggtitle(p_title, paste0("Chromosome ", chrom))
p2 <- p_func(df, "Beagle", "Eagle", pop, chrom = chrom) +
guides(colour="none") + ggtitle("", "")
p3 <- p_func(df, "SHAPEIT", "Eagle", pop, chrom = chrom) +
guides(colour="none") + ggtitle("", "")
return(grid.arrange(p1, p_legend, p2, p3, ncol = 2))
}
plot_total_errors <- function(df, m1, m2, pop, chrom=as.character(chrom)){
p <- df %>%
mutate(Beagle = (n_other_beagle + n_flip_beagle),
Eagle = (n_other_eagle + n_flip_eagle),
SHAPEIT = (n_other_shapeit + n_flip_shapeit)) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Total Errors", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
plot_total_errors_noth <- function(df, m1, m2, pop, chrom=as.character(chrom)){
p <- df %>%
mutate(Beagle = (n_switch_b + n_flip_b),
Eagle = (n_switch_e + n_flip_e),
SHAPEIT = (n_switch_s + n_flip_s)) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Total Errors", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
table_total_errors <- function(df, pop){
res <- df %>%
mutate(Beagle = (n_other_beagle + n_flip_beagle),
Eagle = (n_other_eagle + n_flip_eagle),
SHAPEIT = (n_other_shapeit + n_flip_shapeit)) %>%
mutate(b_l_e = factor(Beagle < Eagle),
b_e_e = factor(Beagle == Eagle),
b_l_s = factor(Beagle < SHAPEIT),
e_l_b = factor(Beagle > Eagle),
e_l_s = factor(Eagle < SHAPEIT),
s_l_b = factor(SHAPEIT < Beagle),
s_l_e = factor(SHAPEIT < Eagle)) %>%
tbl_summary(by = !! sym(pop),
include = c(b_l_e, b_e_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
return(res)
}
table_total_errors_noth <- function(df, pop){
res <- df %>%
mutate(Beagle = (n_switch_b + n_flip_b),
Eagle = (n_switch_e + n_flip_e),
SHAPEIT = (n_switch_s + n_flip_s)) %>%
mutate(b_l_e = factor(Beagle < Eagle),
b_e_e = factor(Beagle == Eagle),
b_l_s = factor(Beagle < SHAPEIT),
e_l_b = factor(Beagle > Eagle),
e_l_s = factor(Eagle < SHAPEIT),
s_l_b = factor(SHAPEIT < Beagle),
s_l_e = factor(SHAPEIT < Eagle)) %>%
tbl_summary(by = !! sym(pop),
include = c(b_l_e, b_e_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
return(res)
}
chrom <- 1
df_switch_trio_noth <- df_switch_trio_noth %>%
left_join({df_subj_rel %>% select(SUPER, id2)}, by = c("sample" = "id2"))
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 187 (93%) | 51 (37%) | 14 (19%) | 34 (32%) | 38 (45%) |
| TRUE | 14 (7.0%) | 86 (63%) | 58 (81%) | 73 (68%) | 47 (55%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 136 (99%) | 71 (99%) | 105 (98%) | 84 (99%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 1 (1.4%) | 2 (1.9%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 11 (5.5%) | 3 (2.2%) | 5 (6.9%) | 8 (7.5%) | 0 (0%) |
| TRUE | 190 (95%) | 134 (98%) | 67 (93%) | 99 (93%) | 85 (100%) |
| e_l_b | |||||
| FALSE | 15 (7.5%) | 87 (64%) | 59 (82%) | 75 (70%) | 48 (56%) |
| TRUE | 186 (93%) | 50 (36%) | 13 (18%) | 32 (30%) | 37 (44%) |
| e_l_s | |||||
| FALSE | 4 (2.0%) | 31 (23%) | 34 (47%) | 31 (29%) | 3 (3.5%) |
| TRUE | 197 (98%) | 106 (77%) | 38 (53%) | 76 (71%) | 82 (96%) |
| s_l_b | |||||
| FALSE | 191 (95%) | 134 (98%) | 67 (93%) | 100 (93%) | 85 (100%) |
| TRUE | 10 (5.0%) | 3 (2.2%) | 5 (6.9%) | 7 (6.5%) | 0 (0%) |
| s_l_e | |||||
| FALSE | 197 (98%) | 108 (79%) | 38 (53%) | 77 (72%) | 82 (96%) |
| TRUE | 4 (2.0%) | 29 (21%) | 34 (47%) | 30 (28%) | 3 (3.5%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 196 (98%) | 73 (53%) | 25 (35%) | 43 (40%) | 46 (54%) |
| TRUE | 5 (2.5%) | 64 (47%) | 47 (65%) | 64 (60%) | 39 (46%) |
| b_e_e | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 9 (4.5%) | 8 (5.8%) | 6 (8.3%) | 19 (18%) | 1 (1.2%) |
| TRUE | 192 (96%) | 129 (94%) | 66 (92%) | 88 (82%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 5 (2.5%) | 64 (47%) | 47 (65%) | 65 (61%) | 39 (46%) |
| TRUE | 196 (98%) | 73 (53%) | 25 (35%) | 42 (39%) | 46 (54%) |
| e_l_s | |||||
| FALSE | 1 (0.5%) | 20 (15%) | 19 (26%) | 23 (21%) | 2 (2.4%) |
| TRUE | 200 (100%) | 117 (85%) | 53 (74%) | 84 (79%) | 83 (98%) |
| s_l_b | |||||
| FALSE | 192 (96%) | 130 (95%) | 66 (92%) | 88 (82%) | 84 (99%) |
| TRUE | 9 (4.5%) | 7 (5.1%) | 6 (8.3%) | 19 (18%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 200 (100%) | 118 (86%) | 54 (75%) | 85 (79%) | 83 (98%) |
| TRUE | 1 (0.5%) | 19 (14%) | 18 (25%) | 22 (21%) | 2 (2.4%) |
| 1 n (%) | |||||
chrom <- 2
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 184 (92%) | 63 (46%) | 15 (21%) | 40 (37%) | 42 (49%) |
| TRUE | 17 (8.5%) | 74 (54%) | 57 (79%) | 67 (63%) | 43 (51%) |
| b_e_e | |||||
| FALSE | 201 (100%) | 135 (99%) | 72 (100%) | 105 (98%) | 84 (99%) |
| TRUE | 0 (0%) | 2 (1.5%) | 0 (0%) | 2 (1.9%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 11 (5.5%) | 8 (5.8%) | 6 (8.3%) | 12 (11%) | 2 (2.4%) |
| TRUE | 190 (95%) | 129 (94%) | 66 (92%) | 95 (89%) | 83 (98%) |
| e_l_b | |||||
| FALSE | 17 (8.5%) | 76 (55%) | 57 (79%) | 69 (64%) | 44 (52%) |
| TRUE | 184 (92%) | 61 (45%) | 15 (21%) | 38 (36%) | 41 (48%) |
| e_l_s | |||||
| FALSE | 1 (0.5%) | 26 (19%) | 19 (26%) | 27 (25%) | 4 (4.7%) |
| TRUE | 200 (100%) | 111 (81%) | 53 (74%) | 80 (75%) | 81 (95%) |
| s_l_b | |||||
| FALSE | 190 (95%) | 130 (95%) | 66 (92%) | 97 (91%) | 83 (98%) |
| TRUE | 11 (5.5%) | 7 (5.1%) | 6 (8.3%) | 10 (9.3%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 200 (100%) | 112 (82%) | 53 (74%) | 82 (77%) | 81 (95%) |
| TRUE | 1 (0.5%) | 25 (18%) | 19 (26%) | 25 (23%) | 4 (4.7%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 186 (93%) | 81 (59%) | 22 (31%) | 60 (56%) | 55 (65%) |
| TRUE | 15 (7.5%) | 56 (41%) | 50 (69%) | 47 (44%) | 30 (35%) |
| b_e_e | |||||
| FALSE | 201 (100%) | 135 (99%) | 70 (97%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 2 (1.5%) | 2 (2.8%) | 1 (0.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 10 (5.0%) | 6 (4.4%) | 1 (1.4%) | 6 (5.6%) | 1 (1.2%) |
| TRUE | 191 (95%) | 131 (96%) | 71 (99%) | 101 (94%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 15 (7.5%) | 58 (42%) | 52 (72%) | 48 (45%) | 30 (35%) |
| TRUE | 186 (93%) | 79 (58%) | 20 (28%) | 59 (55%) | 55 (65%) |
| e_l_s | |||||
| FALSE | 2 (1.0%) | 24 (18%) | 9 (13%) | 11 (10%) | 0 (0%) |
| TRUE | 199 (99%) | 113 (82%) | 63 (88%) | 96 (90%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 192 (96%) | 131 (96%) | 71 (99%) | 101 (94%) | 84 (99%) |
| TRUE | 9 (4.5%) | 6 (4.4%) | 1 (1.4%) | 6 (5.6%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 199 (99%) | 113 (82%) | 63 (88%) | 96 (90%) | 85 (100%) |
| TRUE | 2 (1.0%) | 24 (18%) | 9 (13%) | 11 (10%) | 0 (0%) |
| 1 n (%) | |||||
chrom <- 3
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 187 (93%) | 56 (41%) | 16 (22%) | 34 (32%) | 39 (46%) |
| TRUE | 14 (7.0%) | 81 (59%) | 56 (78%) | 73 (68%) | 46 (54%) |
| b_e_e | |||||
| FALSE | 201 (100%) | 135 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 2 (1.5%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 14 (7.0%) | 7 (5.1%) | 6 (8.3%) | 12 (11%) | 3 (3.5%) |
| TRUE | 187 (93%) | 130 (95%) | 66 (92%) | 95 (89%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 14 (7.0%) | 83 (61%) | 56 (78%) | 74 (69%) | 46 (54%) |
| TRUE | 187 (93%) | 54 (39%) | 16 (22%) | 33 (31%) | 39 (46%) |
| e_l_s | |||||
| FALSE | 1 (0.5%) | 30 (22%) | 25 (35%) | 29 (27%) | 9 (11%) |
| TRUE | 200 (100%) | 107 (78%) | 47 (65%) | 78 (73%) | 76 (89%) |
| s_l_b | |||||
| FALSE | 188 (94%) | 130 (95%) | 66 (92%) | 98 (92%) | 82 (96%) |
| TRUE | 13 (6.5%) | 7 (5.1%) | 6 (8.3%) | 9 (8.4%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 200 (100%) | 108 (79%) | 48 (67%) | 78 (73%) | 76 (89%) |
| TRUE | 1 (0.5%) | 29 (21%) | 24 (33%) | 29 (27%) | 9 (11%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 192 (96%) | 78 (57%) | 24 (33%) | 57 (53%) | 55 (65%) |
| TRUE | 9 (4.5%) | 59 (43%) | 48 (67%) | 50 (47%) | 30 (35%) |
| b_e_e | |||||
| FALSE | 201 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 84 (99%) |
| TRUE | 0 (0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 7 (3.5%) | 8 (5.8%) | 4 (5.6%) | 12 (11%) | 0 (0%) |
| TRUE | 194 (97%) | 129 (94%) | 68 (94%) | 95 (89%) | 85 (100%) |
| e_l_b | |||||
| FALSE | 9 (4.5%) | 61 (45%) | 48 (67%) | 50 (47%) | 31 (36%) |
| TRUE | 192 (96%) | 76 (55%) | 24 (33%) | 57 (53%) | 54 (64%) |
| e_l_s | |||||
| FALSE | 1 (0.5%) | 17 (12%) | 20 (28%) | 14 (13%) | 2 (2.4%) |
| TRUE | 200 (100%) | 120 (88%) | 52 (72%) | 93 (87%) | 83 (98%) |
| s_l_b | |||||
| FALSE | 194 (97%) | 130 (95%) | 68 (94%) | 98 (92%) | 85 (100%) |
| TRUE | 7 (3.5%) | 7 (5.1%) | 4 (5.6%) | 9 (8.4%) | 0 (0%) |
| s_l_e | |||||
| FALSE | 200 (100%) | 121 (88%) | 54 (75%) | 93 (87%) | 83 (98%) |
| TRUE | 1 (0.5%) | 16 (12%) | 18 (25%) | 14 (13%) | 2 (2.4%) |
| 1 n (%) | |||||
chrom <- 4
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 178 (89%) | 56 (41%) | 12 (17%) | 29 (27%) | 37 (44%) |
| TRUE | 23 (11%) | 81 (59%) | 60 (83%) | 78 (73%) | 48 (56%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 16 (8.0%) | 6 (4.4%) | 1 (1.4%) | 14 (13%) | 3 (3.5%) |
| TRUE | 185 (92%) | 131 (96%) | 71 (99%) | 93 (87%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 24 (12%) | 82 (60%) | 60 (83%) | 78 (73%) | 48 (56%) |
| TRUE | 177 (88%) | 55 (40%) | 12 (17%) | 29 (27%) | 37 (44%) |
| e_l_s | |||||
| FALSE | 9 (4.5%) | 28 (20%) | 35 (49%) | 30 (28%) | 4 (4.7%) |
| TRUE | 192 (96%) | 109 (80%) | 37 (51%) | 77 (72%) | 81 (95%) |
| s_l_b | |||||
| FALSE | 186 (93%) | 131 (96%) | 71 (99%) | 93 (87%) | 82 (96%) |
| TRUE | 15 (7.5%) | 6 (4.4%) | 1 (1.4%) | 14 (13%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 192 (96%) | 110 (80%) | 37 (51%) | 77 (72%) | 81 (95%) |
| TRUE | 9 (4.5%) | 27 (20%) | 35 (49%) | 30 (28%) | 4 (4.7%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 188 (94%) | 68 (50%) | 13 (18%) | 47 (44%) | 55 (65%) |
| TRUE | 13 (6.5%) | 69 (50%) | 59 (82%) | 60 (56%) | 30 (35%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 136 (99%) | 72 (100%) | 105 (98%) | 82 (96%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 2 (1.9%) | 3 (3.5%) |
| b_l_s | |||||
| FALSE | 21 (10%) | 12 (8.8%) | 2 (2.8%) | 9 (8.4%) | 3 (3.5%) |
| TRUE | 180 (90%) | 125 (91%) | 70 (97%) | 98 (92%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 14 (7.0%) | 70 (51%) | 59 (82%) | 62 (58%) | 33 (39%) |
| TRUE | 187 (93%) | 67 (49%) | 13 (18%) | 45 (42%) | 52 (61%) |
| e_l_s | |||||
| FALSE | 3 (1.5%) | 24 (18%) | 20 (28%) | 13 (12%) | 5 (5.9%) |
| TRUE | 198 (99%) | 113 (82%) | 52 (72%) | 94 (88%) | 80 (94%) |
| s_l_b | |||||
| FALSE | 180 (90%) | 125 (91%) | 70 (97%) | 98 (92%) | 82 (96%) |
| TRUE | 21 (10%) | 12 (8.8%) | 2 (2.8%) | 9 (8.4%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 198 (99%) | 114 (83%) | 53 (74%) | 94 (88%) | 80 (94%) |
| TRUE | 3 (1.5%) | 23 (17%) | 19 (26%) | 13 (12%) | 5 (5.9%) |
| 1 n (%) | |||||
chrom <- 5
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 186 (93%) | 61 (45%) | 14 (19%) | 46 (43%) | 47 (55%) |
| TRUE | 15 (7.5%) | 76 (55%) | 58 (81%) | 61 (57%) | 38 (45%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 137 (100%) | 71 (99%) | 106 (99%) | 82 (96%) |
| TRUE | 1 (0.5%) | 0 (0%) | 1 (1.4%) | 1 (0.9%) | 3 (3.5%) |
| b_l_s | |||||
| FALSE | 7 (3.5%) | 8 (5.8%) | 5 (6.9%) | 12 (11%) | 2 (2.4%) |
| TRUE | 194 (97%) | 129 (94%) | 67 (93%) | 95 (89%) | 83 (98%) |
| e_l_b | |||||
| FALSE | 16 (8.0%) | 76 (55%) | 59 (82%) | 62 (58%) | 41 (48%) |
| TRUE | 185 (92%) | 61 (45%) | 13 (18%) | 45 (42%) | 44 (52%) |
| e_l_s | |||||
| FALSE | 1 (0.5%) | 20 (15%) | 27 (38%) | 27 (25%) | 5 (5.9%) |
| TRUE | 200 (100%) | 117 (85%) | 45 (63%) | 80 (75%) | 80 (94%) |
| s_l_b | |||||
| FALSE | 194 (97%) | 130 (95%) | 67 (93%) | 96 (90%) | 83 (98%) |
| TRUE | 7 (3.5%) | 7 (5.1%) | 5 (6.9%) | 11 (10%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 200 (100%) | 117 (85%) | 47 (65%) | 81 (76%) | 80 (94%) |
| TRUE | 1 (0.5%) | 20 (15%) | 25 (35%) | 26 (24%) | 5 (5.9%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 189 (94%) | 76 (55%) | 23 (32%) | 57 (53%) | 53 (62%) |
| TRUE | 12 (6.0%) | 61 (45%) | 49 (68%) | 50 (47%) | 32 (38%) |
| b_e_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 72 (100%) | 105 (98%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 0 (0%) | 2 (1.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 17 (8.5%) | 7 (5.1%) | 2 (2.8%) | 12 (11%) | 2 (2.4%) |
| TRUE | 184 (92%) | 130 (95%) | 70 (97%) | 95 (89%) | 83 (98%) |
| e_l_b | |||||
| FALSE | 12 (6.0%) | 64 (47%) | 49 (68%) | 52 (49%) | 32 (38%) |
| TRUE | 189 (94%) | 73 (53%) | 23 (32%) | 55 (51%) | 53 (62%) |
| e_l_s | |||||
| FALSE | 4 (2.0%) | 20 (15%) | 12 (17%) | 22 (21%) | 1 (1.2%) |
| TRUE | 197 (98%) | 117 (85%) | 60 (83%) | 85 (79%) | 84 (99%) |
| s_l_b | |||||
| FALSE | 185 (92%) | 130 (95%) | 70 (97%) | 95 (89%) | 84 (99%) |
| TRUE | 16 (8.0%) | 7 (5.1%) | 2 (2.8%) | 12 (11%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 197 (98%) | 118 (86%) | 60 (83%) | 86 (80%) | 84 (99%) |
| TRUE | 4 (2.0%) | 19 (14%) | 12 (17%) | 21 (20%) | 1 (1.2%) |
| 1 n (%) | |||||
chrom <- 6
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 169 (84%) | 55 (40%) | 12 (17%) | 41 (38%) | 39 (46%) |
| TRUE | 32 (16%) | 82 (60%) | 60 (83%) | 66 (62%) | 46 (54%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 134 (98%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 1 (0.5%) | 3 (2.2%) | 0 (0%) | 0 (0%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 6 (3.0%) | 13 (9.5%) | 3 (4.2%) | 12 (11%) | 3 (3.5%) |
| TRUE | 195 (97%) | 124 (91%) | 69 (96%) | 95 (89%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 33 (16%) | 85 (62%) | 60 (83%) | 66 (62%) | 46 (54%) |
| TRUE | 168 (84%) | 52 (38%) | 12 (17%) | 41 (38%) | 39 (46%) |
| e_l_s | |||||
| FALSE | 6 (3.0%) | 34 (25%) | 32 (44%) | 27 (25%) | 7 (8.2%) |
| TRUE | 195 (97%) | 103 (75%) | 40 (56%) | 80 (75%) | 78 (92%) |
| s_l_b | |||||
| FALSE | 195 (97%) | 124 (91%) | 69 (96%) | 96 (90%) | 83 (98%) |
| TRUE | 6 (3.0%) | 13 (9.5%) | 3 (4.2%) | 11 (10%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 195 (97%) | 104 (76%) | 42 (58%) | 83 (78%) | 78 (92%) |
| TRUE | 6 (3.0%) | 33 (24%) | 30 (42%) | 24 (22%) | 7 (8.2%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 185 (92%) | 74 (54%) | 18 (25%) | 53 (50%) | 49 (58%) |
| TRUE | 16 (8.0%) | 63 (46%) | 54 (75%) | 54 (50%) | 36 (42%) |
| b_e_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 71 (99%) | 105 (98%) | 84 (99%) |
| TRUE | 0 (0%) | 3 (2.2%) | 1 (1.4%) | 2 (1.9%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 12 (6.0%) | 9 (6.6%) | 5 (6.9%) | 13 (12%) | 4 (4.7%) |
| TRUE | 189 (94%) | 128 (93%) | 67 (93%) | 94 (88%) | 81 (95%) |
| e_l_b | |||||
| FALSE | 16 (8.0%) | 66 (48%) | 55 (76%) | 56 (52%) | 37 (44%) |
| TRUE | 185 (92%) | 71 (52%) | 17 (24%) | 51 (48%) | 48 (56%) |
| e_l_s | |||||
| FALSE | 3 (1.5%) | 28 (20%) | 22 (31%) | 20 (19%) | 3 (3.5%) |
| TRUE | 198 (99%) | 109 (80%) | 50 (69%) | 87 (81%) | 82 (96%) |
| s_l_b | |||||
| FALSE | 190 (95%) | 128 (93%) | 67 (93%) | 95 (89%) | 82 (96%) |
| TRUE | 11 (5.5%) | 9 (6.6%) | 5 (6.9%) | 12 (11%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 198 (99%) | 110 (80%) | 52 (72%) | 90 (84%) | 83 (98%) |
| TRUE | 3 (1.5%) | 27 (20%) | 20 (28%) | 17 (16%) | 2 (2.4%) |
| 1 n (%) | |||||
chrom <- 7
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 172 (86%) | 51 (37%) | 13 (18%) | 33 (31%) | 35 (41%) |
| TRUE | 29 (14%) | 86 (63%) | 59 (82%) | 74 (69%) | 50 (59%) |
| b_e_e | |||||
| FALSE | 198 (99%) | 137 (100%) | 72 (100%) | 104 (97%) | 85 (100%) |
| TRUE | 3 (1.5%) | 0 (0%) | 0 (0%) | 3 (2.8%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 27 (13%) | 2 (1.5%) | 4 (5.6%) | 20 (19%) | 2 (2.4%) |
| TRUE | 174 (87%) | 135 (99%) | 68 (94%) | 87 (81%) | 83 (98%) |
| e_l_b | |||||
| FALSE | 32 (16%) | 86 (63%) | 59 (82%) | 77 (72%) | 50 (59%) |
| TRUE | 169 (84%) | 51 (37%) | 13 (18%) | 30 (28%) | 35 (41%) |
| e_l_s | |||||
| FALSE | 5 (2.5%) | 30 (22%) | 31 (43%) | 43 (40%) | 11 (13%) |
| TRUE | 196 (98%) | 107 (78%) | 41 (57%) | 64 (60%) | 74 (87%) |
| s_l_b | |||||
| FALSE | 176 (88%) | 135 (99%) | 68 (94%) | 87 (81%) | 83 (98%) |
| TRUE | 25 (12%) | 2 (1.5%) | 4 (5.6%) | 20 (19%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 196 (98%) | 108 (79%) | 43 (60%) | 64 (60%) | 74 (87%) |
| TRUE | 5 (2.5%) | 29 (21%) | 29 (40%) | 43 (40%) | 11 (13%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 177 (88%) | 75 (55%) | 28 (39%) | 44 (41%) | 53 (62%) |
| TRUE | 24 (12%) | 62 (45%) | 44 (61%) | 63 (59%) | 32 (38%) |
| b_e_e | |||||
| FALSE | 199 (99%) | 135 (99%) | 72 (100%) | 107 (100%) | 83 (98%) |
| TRUE | 2 (1.0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 23 (11%) | 11 (8.0%) | 6 (8.3%) | 19 (18%) | 2 (2.4%) |
| TRUE | 178 (89%) | 126 (92%) | 66 (92%) | 88 (82%) | 83 (98%) |
| e_l_b | |||||
| FALSE | 26 (13%) | 64 (47%) | 44 (61%) | 63 (59%) | 34 (40%) |
| TRUE | 175 (87%) | 73 (53%) | 28 (39%) | 44 (41%) | 51 (60%) |
| e_l_s | |||||
| FALSE | 2 (1.0%) | 26 (19%) | 17 (24%) | 26 (24%) | 3 (3.5%) |
| TRUE | 199 (99%) | 111 (81%) | 55 (76%) | 81 (76%) | 82 (96%) |
| s_l_b | |||||
| FALSE | 178 (89%) | 126 (92%) | 66 (92%) | 89 (83%) | 83 (98%) |
| TRUE | 23 (11%) | 11 (8.0%) | 6 (8.3%) | 18 (17%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 199 (99%) | 112 (82%) | 55 (76%) | 82 (77%) | 82 (96%) |
| TRUE | 2 (1.0%) | 25 (18%) | 17 (24%) | 25 (23%) | 3 (3.5%) |
| 1 n (%) | |||||
chrom <- 8
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 47 (23%) | 9 (6.6%) | 1 (1.4%) | 2 (1.9%) | 5 (5.9%) |
| TRUE | 154 (77%) | 128 (93%) | 71 (99%) | 105 (98%) | 80 (94%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 133 (66%) | 79 (58%) | 60 (83%) | 67 (63%) | 50 (59%) |
| TRUE | 68 (34%) | 58 (42%) | 12 (17%) | 40 (37%) | 35 (41%) |
| e_l_b | |||||
| FALSE | 155 (77%) | 129 (94%) | 71 (99%) | 105 (98%) | 80 (94%) |
| TRUE | 46 (23%) | 8 (5.8%) | 1 (1.4%) | 2 (1.9%) | 5 (5.9%) |
| e_l_s | |||||
| FALSE | 144 (72%) | 110 (80%) | 71 (99%) | 88 (82%) | 56 (66%) |
| TRUE | 57 (28%) | 27 (20%) | 1 (1.4%) | 19 (18%) | 29 (34%) |
| s_l_b | |||||
| FALSE | 71 (35%) | 62 (45%) | 14 (19%) | 43 (40%) | 36 (42%) |
| TRUE | 130 (65%) | 75 (55%) | 58 (81%) | 64 (60%) | 49 (58%) |
| s_l_e | |||||
| FALSE | 58 (29%) | 27 (20%) | 1 (1.4%) | 19 (18%) | 29 (34%) |
| TRUE | 143 (71%) | 110 (80%) | 71 (99%) | 88 (82%) | 56 (66%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 187 (93%) | 68 (50%) | 28 (39%) | 58 (54%) | 53 (62%) |
| TRUE | 14 (7.0%) | 69 (50%) | 44 (61%) | 49 (46%) | 32 (38%) |
| b_e_e | |||||
| FALSE | 201 (100%) | 135 (99%) | 70 (97%) | 107 (100%) | 84 (99%) |
| TRUE | 0 (0%) | 2 (1.5%) | 2 (2.8%) | 0 (0%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 16 (8.0%) | 11 (8.0%) | 16 (22%) | 15 (14%) | 6 (7.1%) |
| TRUE | 185 (92%) | 126 (92%) | 56 (78%) | 92 (86%) | 79 (93%) |
| e_l_b | |||||
| FALSE | 14 (7.0%) | 71 (52%) | 46 (64%) | 49 (46%) | 33 (39%) |
| TRUE | 187 (93%) | 66 (48%) | 26 (36%) | 58 (54%) | 52 (61%) |
| e_l_s | |||||
| FALSE | 1 (0.5%) | 20 (15%) | 23 (32%) | 25 (23%) | 4 (4.7%) |
| TRUE | 200 (100%) | 117 (85%) | 49 (68%) | 82 (77%) | 81 (95%) |
| s_l_b | |||||
| FALSE | 187 (93%) | 126 (92%) | 56 (78%) | 92 (86%) | 80 (94%) |
| TRUE | 14 (7.0%) | 11 (8.0%) | 16 (22%) | 15 (14%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 200 (100%) | 118 (86%) | 51 (71%) | 82 (77%) | 81 (95%) |
| TRUE | 1 (0.5%) | 19 (14%) | 21 (29%) | 25 (23%) | 4 (4.7%) |
| 1 n (%) | |||||
chrom <- 9
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 166 (83%) | 58 (42%) | 13 (18%) | 39 (36%) | 48 (56%) |
| TRUE | 35 (17%) | 79 (58%) | 59 (82%) | 68 (64%) | 37 (44%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 137 (100%) | 72 (100%) | 104 (97%) | 85 (100%) |
| TRUE | 1 (0.5%) | 0 (0%) | 0 (0%) | 3 (2.8%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 33 (16%) | 16 (12%) | 9 (13%) | 23 (21%) | 8 (9.4%) |
| TRUE | 168 (84%) | 121 (88%) | 63 (88%) | 84 (79%) | 77 (91%) |
| e_l_b | |||||
| FALSE | 36 (18%) | 79 (58%) | 59 (82%) | 71 (66%) | 37 (44%) |
| TRUE | 165 (82%) | 58 (42%) | 13 (18%) | 36 (34%) | 48 (56%) |
| e_l_s | |||||
| FALSE | 14 (7.0%) | 30 (22%) | 32 (44%) | 43 (40%) | 9 (11%) |
| TRUE | 187 (93%) | 107 (78%) | 40 (56%) | 64 (60%) | 76 (89%) |
| s_l_b | |||||
| FALSE | 170 (85%) | 121 (88%) | 63 (88%) | 85 (79%) | 78 (92%) |
| TRUE | 31 (15%) | 16 (12%) | 9 (13%) | 22 (21%) | 7 (8.2%) |
| s_l_e | |||||
| FALSE | 188 (94%) | 107 (78%) | 41 (57%) | 67 (63%) | 77 (91%) |
| TRUE | 13 (6.5%) | 30 (22%) | 31 (43%) | 40 (37%) | 8 (9.4%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 181 (90%) | 73 (53%) | 18 (25%) | 51 (48%) | 53 (62%) |
| TRUE | 20 (10.0%) | 64 (47%) | 54 (75%) | 56 (52%) | 32 (38%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 136 (99%) | 72 (100%) | 105 (98%) | 85 (100%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 2 (1.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 29 (14%) | 10 (7.3%) | 8 (11%) | 18 (17%) | 8 (9.4%) |
| TRUE | 172 (86%) | 127 (93%) | 64 (89%) | 89 (83%) | 77 (91%) |
| e_l_b | |||||
| FALSE | 21 (10%) | 65 (47%) | 54 (75%) | 58 (54%) | 32 (38%) |
| TRUE | 180 (90%) | 72 (53%) | 18 (25%) | 49 (46%) | 53 (62%) |
| e_l_s | |||||
| FALSE | 6 (3.0%) | 19 (14%) | 22 (31%) | 36 (34%) | 2 (2.4%) |
| TRUE | 195 (97%) | 118 (86%) | 50 (69%) | 71 (66%) | 83 (98%) |
| s_l_b | |||||
| FALSE | 174 (87%) | 127 (93%) | 65 (90%) | 89 (83%) | 79 (93%) |
| TRUE | 27 (13%) | 10 (7.3%) | 7 (9.7%) | 18 (17%) | 6 (7.1%) |
| s_l_e | |||||
| FALSE | 195 (97%) | 118 (86%) | 50 (69%) | 72 (67%) | 83 (98%) |
| TRUE | 6 (3.0%) | 19 (14%) | 22 (31%) | 35 (33%) | 2 (2.4%) |
| 1 n (%) | |||||
chrom <- 10
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 162 (81%) | 43 (31%) | 12 (17%) | 37 (35%) | 29 (34%) |
| TRUE | 39 (19%) | 94 (69%) | 60 (83%) | 70 (65%) | 56 (66%) |
| b_e_e | |||||
| FALSE | 196 (98%) | 135 (99%) | 70 (97%) | 106 (99%) | 85 (100%) |
| TRUE | 5 (2.5%) | 2 (1.5%) | 2 (2.8%) | 1 (0.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 19 (9.5%) | 12 (8.8%) | 10 (14%) | 23 (21%) | 3 (3.5%) |
| TRUE | 182 (91%) | 125 (91%) | 62 (86%) | 84 (79%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 44 (22%) | 96 (70%) | 62 (86%) | 71 (66%) | 56 (66%) |
| TRUE | 157 (78%) | 41 (30%) | 10 (14%) | 36 (34%) | 29 (34%) |
| e_l_s | |||||
| FALSE | 8 (4.0%) | 43 (31%) | 32 (44%) | 40 (37%) | 14 (16%) |
| TRUE | 193 (96%) | 94 (69%) | 40 (56%) | 67 (63%) | 71 (84%) |
| s_l_b | |||||
| FALSE | 182 (91%) | 128 (93%) | 62 (86%) | 86 (80%) | 82 (96%) |
| TRUE | 19 (9.5%) | 9 (6.6%) | 10 (14%) | 21 (20%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 193 (96%) | 94 (69%) | 41 (57%) | 70 (65%) | 71 (84%) |
| TRUE | 8 (4.0%) | 43 (31%) | 31 (43%) | 37 (35%) | 14 (16%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 183 (91%) | 68 (50%) | 21 (29%) | 43 (40%) | 39 (46%) |
| TRUE | 18 (9.0%) | 69 (50%) | 51 (71%) | 64 (60%) | 46 (54%) |
| b_e_e | |||||
| FALSE | 199 (99%) | 137 (100%) | 71 (99%) | 107 (100%) | 83 (98%) |
| TRUE | 2 (1.0%) | 0 (0%) | 1 (1.4%) | 0 (0%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 19 (9.5%) | 17 (12%) | 4 (5.6%) | 18 (17%) | 5 (5.9%) |
| TRUE | 182 (91%) | 120 (88%) | 68 (94%) | 89 (83%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 20 (10.0%) | 69 (50%) | 52 (72%) | 64 (60%) | 48 (56%) |
| TRUE | 181 (90%) | 68 (50%) | 20 (28%) | 43 (40%) | 37 (44%) |
| e_l_s | |||||
| FALSE | 2 (1.0%) | 26 (19%) | 25 (35%) | 28 (26%) | 9 (11%) |
| TRUE | 199 (99%) | 111 (81%) | 47 (65%) | 79 (74%) | 76 (89%) |
| s_l_b | |||||
| FALSE | 182 (91%) | 123 (90%) | 68 (94%) | 89 (83%) | 80 (94%) |
| TRUE | 19 (9.5%) | 14 (10%) | 4 (5.6%) | 18 (17%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 199 (99%) | 111 (81%) | 48 (67%) | 79 (74%) | 76 (89%) |
| TRUE | 2 (1.0%) | 26 (19%) | 24 (33%) | 28 (26%) | 9 (11%) |
| 1 n (%) | |||||
chrom <- 10
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
| b3306a4 | theandyb | 2025-06-19 |
| 01d26a4 | theandyb | 2025-06-18 |
| fc667bc | theandyb | 2025-06-18 |
| c2bd645 | theandyb | 2025-06-16 |
| 1243aea | Andy Beck | 2024-07-03 |
| 292c663 | Andy Beck | 2024-06-13 |
| ec0ba0b | Andy Beck | 2024-05-29 |
| 9a4bd3e | Andy Beck | 2024-05-29 |
| 34c040a | Andy Beck | 2024-05-29 |
| d6dca59 | Andy Beck | 2024-05-29 |
| 8041a90 | Andy Beck | 2024-05-29 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 162 (81%) | 43 (31%) | 12 (17%) | 37 (35%) | 29 (34%) |
| TRUE | 39 (19%) | 94 (69%) | 60 (83%) | 70 (65%) | 56 (66%) |
| b_e_e | |||||
| FALSE | 196 (98%) | 135 (99%) | 70 (97%) | 106 (99%) | 85 (100%) |
| TRUE | 5 (2.5%) | 2 (1.5%) | 2 (2.8%) | 1 (0.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 19 (9.5%) | 12 (8.8%) | 10 (14%) | 23 (21%) | 3 (3.5%) |
| TRUE | 182 (91%) | 125 (91%) | 62 (86%) | 84 (79%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 44 (22%) | 96 (70%) | 62 (86%) | 71 (66%) | 56 (66%) |
| TRUE | 157 (78%) | 41 (30%) | 10 (14%) | 36 (34%) | 29 (34%) |
| e_l_s | |||||
| FALSE | 8 (4.0%) | 43 (31%) | 32 (44%) | 40 (37%) | 14 (16%) |
| TRUE | 193 (96%) | 94 (69%) | 40 (56%) | 67 (63%) | 71 (84%) |
| s_l_b | |||||
| FALSE | 182 (91%) | 128 (93%) | 62 (86%) | 86 (80%) | 82 (96%) |
| TRUE | 19 (9.5%) | 9 (6.6%) | 10 (14%) | 21 (20%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 193 (96%) | 94 (69%) | 41 (57%) | 70 (65%) | 71 (84%) |
| TRUE | 8 (4.0%) | 43 (31%) | 31 (43%) | 37 (35%) | 14 (16%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 183 (91%) | 68 (50%) | 21 (29%) | 43 (40%) | 39 (46%) |
| TRUE | 18 (9.0%) | 69 (50%) | 51 (71%) | 64 (60%) | 46 (54%) |
| b_e_e | |||||
| FALSE | 199 (99%) | 137 (100%) | 71 (99%) | 107 (100%) | 83 (98%) |
| TRUE | 2 (1.0%) | 0 (0%) | 1 (1.4%) | 0 (0%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 19 (9.5%) | 17 (12%) | 4 (5.6%) | 18 (17%) | 5 (5.9%) |
| TRUE | 182 (91%) | 120 (88%) | 68 (94%) | 89 (83%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 20 (10.0%) | 69 (50%) | 52 (72%) | 64 (60%) | 48 (56%) |
| TRUE | 181 (90%) | 68 (50%) | 20 (28%) | 43 (40%) | 37 (44%) |
| e_l_s | |||||
| FALSE | 2 (1.0%) | 26 (19%) | 25 (35%) | 28 (26%) | 9 (11%) |
| TRUE | 199 (99%) | 111 (81%) | 47 (65%) | 79 (74%) | 76 (89%) |
| s_l_b | |||||
| FALSE | 182 (91%) | 123 (90%) | 68 (94%) | 89 (83%) | 80 (94%) |
| TRUE | 19 (9.5%) | 14 (10%) | 4 (5.6%) | 18 (17%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 199 (99%) | 111 (81%) | 48 (67%) | 79 (74%) | 76 (89%) |
| TRUE | 2 (1.0%) | 26 (19%) | 24 (33%) | 28 (26%) | 9 (11%) |
| 1 n (%) | |||||
chrom <- 12
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
| b3306a4 | theandyb | 2025-06-19 |
| 01d26a4 | theandyb | 2025-06-18 |
| fc667bc | theandyb | 2025-06-18 |
| c2bd645 | theandyb | 2025-06-16 |
| 1243aea | Andy Beck | 2024-07-03 |
| 76e67f9 | Andy Beck | 2024-06-26 |
| 292c663 | Andy Beck | 2024-06-13 |
| ec0ba0b | Andy Beck | 2024-05-29 |
| 9a4bd3e | Andy Beck | 2024-05-29 |
| d6dca59 | Andy Beck | 2024-05-29 |
| 8041a90 | Andy Beck | 2024-05-29 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 179 (89%) | 52 (38%) | 12 (17%) | 38 (36%) | 43 (51%) |
| TRUE | 22 (11%) | 85 (62%) | 60 (83%) | 69 (64%) | 42 (49%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 135 (99%) | 71 (99%) | 105 (98%) | 85 (100%) |
| TRUE | 1 (0.5%) | 2 (1.5%) | 1 (1.4%) | 2 (1.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 29 (14%) | 10 (7.3%) | 9 (13%) | 13 (12%) | 5 (5.9%) |
| TRUE | 172 (86%) | 127 (93%) | 63 (88%) | 94 (88%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 23 (11%) | 87 (64%) | 61 (85%) | 71 (66%) | 42 (49%) |
| TRUE | 178 (89%) | 50 (36%) | 11 (15%) | 36 (34%) | 43 (51%) |
| e_l_s | |||||
| FALSE | 8 (4.0%) | 30 (22%) | 27 (38%) | 35 (33%) | 9 (11%) |
| TRUE | 193 (96%) | 107 (78%) | 45 (63%) | 72 (67%) | 76 (89%) |
| s_l_b | |||||
| FALSE | 174 (87%) | 128 (93%) | 63 (88%) | 95 (89%) | 80 (94%) |
| TRUE | 27 (13%) | 9 (6.6%) | 9 (13%) | 12 (11%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 194 (97%) | 108 (79%) | 47 (65%) | 72 (67%) | 77 (91%) |
| TRUE | 7 (3.5%) | 29 (21%) | 25 (35%) | 35 (33%) | 8 (9.4%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 190 (95%) | 65 (47%) | 23 (32%) | 53 (50%) | 59 (69%) |
| TRUE | 11 (5.5%) | 72 (53%) | 49 (68%) | 54 (50%) | 26 (31%) |
| b_e_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 71 (99%) | 102 (95%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 1 (1.4%) | 5 (4.7%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 15 (7.5%) | 10 (7.3%) | 8 (11%) | 10 (9.3%) | 5 (5.9%) |
| TRUE | 186 (93%) | 127 (93%) | 64 (89%) | 97 (91%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 11 (5.5%) | 75 (55%) | 50 (69%) | 59 (55%) | 26 (31%) |
| TRUE | 190 (95%) | 62 (45%) | 22 (31%) | 48 (45%) | 59 (69%) |
| e_l_s | |||||
| FALSE | 1 (0.5%) | 19 (14%) | 17 (24%) | 20 (19%) | 3 (3.5%) |
| TRUE | 200 (100%) | 118 (86%) | 55 (76%) | 87 (81%) | 82 (96%) |
| s_l_b | |||||
| FALSE | 189 (94%) | 129 (94%) | 65 (90%) | 98 (92%) | 80 (94%) |
| TRUE | 12 (6.0%) | 8 (5.8%) | 7 (9.7%) | 9 (8.4%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 200 (100%) | 119 (87%) | 55 (76%) | 87 (81%) | 82 (96%) |
| TRUE | 1 (0.5%) | 18 (13%) | 17 (24%) | 20 (19%) | 3 (3.5%) |
| 1 n (%) | |||||
chrom <- 13
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
| b3306a4 | theandyb | 2025-06-19 |
| 01d26a4 | theandyb | 2025-06-18 |
| fc667bc | theandyb | 2025-06-18 |
| c2bd645 | theandyb | 2025-06-16 |
| 1243aea | Andy Beck | 2024-07-03 |
| 76e67f9 | Andy Beck | 2024-06-26 |
| 292c663 | Andy Beck | 2024-06-13 |
| 9a4bd3e | Andy Beck | 2024-05-29 |
| 34c040a | Andy Beck | 2024-05-29 |
| d6dca59 | Andy Beck | 2024-05-29 |
| 8041a90 | Andy Beck | 2024-05-29 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 162 (81%) | 55 (40%) | 12 (17%) | 36 (34%) | 33 (39%) |
| TRUE | 39 (19%) | 82 (60%) | 60 (83%) | 71 (66%) | 52 (61%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 1 (0.5%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 24 (12%) | 14 (10%) | 14 (19%) | 25 (23%) | 8 (9.4%) |
| TRUE | 177 (88%) | 123 (90%) | 58 (81%) | 82 (77%) | 77 (91%) |
| e_l_b | |||||
| FALSE | 40 (20%) | 84 (61%) | 60 (83%) | 71 (66%) | 52 (61%) |
| TRUE | 161 (80%) | 53 (39%) | 12 (17%) | 36 (34%) | 33 (39%) |
| e_l_s | |||||
| FALSE | 8 (4.0%) | 38 (28%) | 41 (57%) | 47 (44%) | 15 (18%) |
| TRUE | 193 (96%) | 99 (72%) | 31 (43%) | 60 (56%) | 70 (82%) |
| s_l_b | |||||
| FALSE | 178 (89%) | 123 (90%) | 59 (82%) | 84 (79%) | 78 (92%) |
| TRUE | 23 (11%) | 14 (10%) | 13 (18%) | 23 (21%) | 7 (8.2%) |
| s_l_e | |||||
| FALSE | 193 (96%) | 100 (73%) | 33 (46%) | 63 (59%) | 72 (85%) |
| TRUE | 8 (4.0%) | 37 (27%) | 39 (54%) | 44 (41%) | 13 (15%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 179 (89%) | 80 (58%) | 19 (26%) | 53 (50%) | 41 (48%) |
| TRUE | 22 (11%) | 57 (42%) | 53 (74%) | 54 (50%) | 44 (52%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 136 (99%) | 71 (99%) | 104 (97%) | 83 (98%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 1 (1.4%) | 3 (2.8%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 23 (11%) | 11 (8.0%) | 11 (15%) | 20 (19%) | 9 (11%) |
| TRUE | 178 (89%) | 126 (92%) | 61 (85%) | 87 (81%) | 76 (89%) |
| e_l_b | |||||
| FALSE | 23 (11%) | 58 (42%) | 54 (75%) | 57 (53%) | 46 (54%) |
| TRUE | 178 (89%) | 79 (58%) | 18 (25%) | 50 (47%) | 39 (46%) |
| e_l_s | |||||
| FALSE | 3 (1.5%) | 27 (20%) | 27 (38%) | 27 (25%) | 10 (12%) |
| TRUE | 198 (99%) | 110 (80%) | 45 (63%) | 80 (75%) | 75 (88%) |
| s_l_b | |||||
| FALSE | 181 (90%) | 128 (93%) | 61 (85%) | 88 (82%) | 76 (89%) |
| TRUE | 20 (10.0%) | 9 (6.6%) | 11 (15%) | 19 (18%) | 9 (11%) |
| s_l_e | |||||
| FALSE | 198 (99%) | 112 (82%) | 45 (63%) | 82 (77%) | 76 (89%) |
| TRUE | 3 (1.5%) | 25 (18%) | 27 (38%) | 25 (23%) | 9 (11%) |
| 1 n (%) | |||||
chrom <- 14
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
| b3306a4 | theandyb | 2025-06-19 |
| 01d26a4 | theandyb | 2025-06-18 |
| c2bd645 | theandyb | 2025-06-16 |
| 1243aea | Andy Beck | 2024-07-03 |
| 292c663 | Andy Beck | 2024-06-13 |
| 9a4bd3e | Andy Beck | 2024-05-29 |
| 34c040a | Andy Beck | 2024-05-29 |
| d6dca59 | Andy Beck | 2024-05-29 |
| 8041a90 | Andy Beck | 2024-05-29 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 159 (79%) | 52 (38%) | 11 (15%) | 36 (34%) | 32 (38%) |
| TRUE | 42 (21%) | 85 (62%) | 61 (85%) | 71 (66%) | 53 (62%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 136 (99%) | 72 (100%) | 103 (96%) | 83 (98%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 4 (3.7%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 28 (14%) | 24 (18%) | 9 (13%) | 25 (23%) | 6 (7.1%) |
| TRUE | 173 (86%) | 113 (82%) | 63 (88%) | 82 (77%) | 79 (93%) |
| e_l_b | |||||
| FALSE | 43 (21%) | 86 (63%) | 61 (85%) | 75 (70%) | 55 (65%) |
| TRUE | 158 (79%) | 51 (37%) | 11 (15%) | 32 (30%) | 30 (35%) |
| e_l_s | |||||
| FALSE | 8 (4.0%) | 45 (33%) | 37 (51%) | 42 (39%) | 12 (14%) |
| TRUE | 193 (96%) | 92 (67%) | 35 (49%) | 65 (61%) | 73 (86%) |
| s_l_b | |||||
| FALSE | 176 (88%) | 114 (83%) | 64 (89%) | 84 (79%) | 80 (94%) |
| TRUE | 25 (12%) | 23 (17%) | 8 (11%) | 23 (21%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 193 (96%) | 93 (68%) | 35 (49%) | 67 (63%) | 74 (87%) |
| TRUE | 8 (4.0%) | 44 (32%) | 37 (51%) | 40 (37%) | 11 (13%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 165 (82%) | 66 (48%) | 21 (29%) | 41 (38%) | 45 (53%) |
| TRUE | 36 (18%) | 71 (52%) | 51 (71%) | 66 (62%) | 40 (47%) |
| b_e_e | |||||
| FALSE | 199 (99%) | 131 (96%) | 72 (100%) | 105 (98%) | 85 (100%) |
| TRUE | 2 (1.0%) | 6 (4.4%) | 0 (0%) | 2 (1.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 23 (11%) | 12 (8.8%) | 6 (8.3%) | 16 (15%) | 3 (3.5%) |
| TRUE | 178 (89%) | 125 (91%) | 66 (92%) | 91 (85%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 38 (19%) | 77 (56%) | 51 (71%) | 68 (64%) | 40 (47%) |
| TRUE | 163 (81%) | 60 (44%) | 21 (29%) | 39 (36%) | 45 (53%) |
| e_l_s | |||||
| FALSE | 8 (4.0%) | 24 (18%) | 29 (40%) | 31 (29%) | 7 (8.2%) |
| TRUE | 193 (96%) | 113 (82%) | 43 (60%) | 76 (71%) | 78 (92%) |
| s_l_b | |||||
| FALSE | 178 (89%) | 126 (92%) | 66 (92%) | 92 (86%) | 82 (96%) |
| TRUE | 23 (11%) | 11 (8.0%) | 6 (8.3%) | 15 (14%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 195 (97%) | 113 (82%) | 44 (61%) | 76 (71%) | 78 (92%) |
| TRUE | 6 (3.0%) | 24 (18%) | 28 (39%) | 31 (29%) | 7 (8.2%) |
| 1 n (%) | |||||
chrom <- 15
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 140 (70%) | 50 (36%) | 12 (17%) | 35 (33%) | 42 (49%) |
| TRUE | 61 (30%) | 87 (64%) | 60 (83%) | 72 (67%) | 43 (51%) |
| b_e_e | |||||
| FALSE | 198 (99%) | 137 (100%) | 71 (99%) | 103 (96%) | 83 (98%) |
| TRUE | 3 (1.5%) | 0 (0%) | 1 (1.4%) | 4 (3.7%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 27 (13%) | 13 (9.5%) | 18 (25%) | 28 (26%) | 8 (9.4%) |
| TRUE | 174 (87%) | 124 (91%) | 54 (75%) | 79 (74%) | 77 (91%) |
| e_l_b | |||||
| FALSE | 64 (32%) | 87 (64%) | 61 (85%) | 76 (71%) | 45 (53%) |
| TRUE | 137 (68%) | 50 (36%) | 11 (15%) | 31 (29%) | 40 (47%) |
| e_l_s | |||||
| FALSE | 22 (11%) | 36 (26%) | 31 (43%) | 48 (45%) | 17 (20%) |
| TRUE | 179 (89%) | 101 (74%) | 41 (57%) | 59 (55%) | 68 (80%) |
| s_l_b | |||||
| FALSE | 175 (87%) | 124 (91%) | 56 (78%) | 81 (76%) | 77 (91%) |
| TRUE | 26 (13%) | 13 (9.5%) | 16 (22%) | 26 (24%) | 8 (9.4%) |
| s_l_e | |||||
| FALSE | 180 (90%) | 103 (75%) | 42 (58%) | 62 (58%) | 70 (82%) |
| TRUE | 21 (10%) | 34 (25%) | 30 (42%) | 45 (42%) | 15 (18%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 153 (76%) | 68 (50%) | 27 (38%) | 51 (48%) | 32 (38%) |
| TRUE | 48 (24%) | 69 (50%) | 45 (63%) | 56 (52%) | 53 (62%) |
| b_e_e | |||||
| FALSE | 198 (99%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 3 (1.5%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 20 (10.0%) | 14 (10%) | 14 (19%) | 26 (24%) | 4 (4.7%) |
| TRUE | 181 (90%) | 123 (90%) | 58 (81%) | 81 (76%) | 81 (95%) |
| e_l_b | |||||
| FALSE | 51 (25%) | 69 (50%) | 45 (63%) | 56 (52%) | 53 (62%) |
| TRUE | 150 (75%) | 68 (50%) | 27 (38%) | 51 (48%) | 32 (38%) |
| e_l_s | |||||
| FALSE | 14 (7.0%) | 28 (20%) | 20 (28%) | 34 (32%) | 12 (14%) |
| TRUE | 187 (93%) | 109 (80%) | 52 (72%) | 73 (68%) | 73 (86%) |
| s_l_b | |||||
| FALSE | 182 (91%) | 124 (91%) | 59 (82%) | 82 (77%) | 81 (95%) |
| TRUE | 19 (9.5%) | 13 (9.5%) | 13 (18%) | 25 (23%) | 4 (4.7%) |
| s_l_e | |||||
| FALSE | 188 (94%) | 110 (80%) | 53 (74%) | 74 (69%) | 75 (88%) |
| TRUE | 13 (6.5%) | 27 (20%) | 19 (26%) | 33 (31%) | 10 (12%) |
| 1 n (%) | |||||
chrom <- 16
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 146 (73%) | 60 (44%) | 18 (25%) | 24 (22%) | 38 (45%) |
| TRUE | 55 (27%) | 77 (56%) | 54 (75%) | 83 (78%) | 47 (55%) |
| b_e_e | |||||
| FALSE | 199 (99%) | 136 (99%) | 72 (100%) | 107 (100%) | 81 (95%) |
| TRUE | 2 (1.0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 4 (4.7%) |
| b_l_s | |||||
| FALSE | 28 (14%) | 15 (11%) | 10 (14%) | 18 (17%) | 7 (8.2%) |
| TRUE | 173 (86%) | 122 (89%) | 62 (86%) | 89 (83%) | 78 (92%) |
| e_l_b | |||||
| FALSE | 57 (28%) | 78 (57%) | 54 (75%) | 83 (78%) | 51 (60%) |
| TRUE | 144 (72%) | 59 (43%) | 18 (25%) | 24 (22%) | 34 (40%) |
| e_l_s | |||||
| FALSE | 15 (7.5%) | 31 (23%) | 32 (44%) | 45 (42%) | 14 (16%) |
| TRUE | 186 (93%) | 106 (77%) | 40 (56%) | 62 (58%) | 71 (84%) |
| s_l_b | |||||
| FALSE | 175 (87%) | 122 (89%) | 63 (88%) | 89 (83%) | 78 (92%) |
| TRUE | 26 (13%) | 15 (11%) | 9 (13%) | 18 (17%) | 7 (8.2%) |
| s_l_e | |||||
| FALSE | 187 (93%) | 107 (78%) | 42 (58%) | 63 (59%) | 72 (85%) |
| TRUE | 14 (7.0%) | 30 (22%) | 30 (42%) | 44 (41%) | 13 (15%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 155 (77%) | 71 (52%) | 24 (33%) | 41 (38%) | 52 (61%) |
| TRUE | 46 (23%) | 66 (48%) | 48 (67%) | 66 (62%) | 33 (39%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 136 (99%) | 72 (100%) | 104 (97%) | 85 (100%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 3 (2.8%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 23 (11%) | 14 (10%) | 13 (18%) | 18 (17%) | 9 (11%) |
| TRUE | 178 (89%) | 123 (90%) | 59 (82%) | 89 (83%) | 76 (89%) |
| e_l_b | |||||
| FALSE | 47 (23%) | 67 (49%) | 48 (67%) | 69 (64%) | 33 (39%) |
| TRUE | 154 (77%) | 70 (51%) | 24 (33%) | 38 (36%) | 52 (61%) |
| e_l_s | |||||
| FALSE | 13 (6.5%) | 19 (14%) | 25 (35%) | 35 (33%) | 6 (7.1%) |
| TRUE | 188 (94%) | 118 (86%) | 47 (65%) | 72 (67%) | 79 (93%) |
| s_l_b | |||||
| FALSE | 180 (90%) | 124 (91%) | 59 (82%) | 91 (85%) | 77 (91%) |
| TRUE | 21 (10%) | 13 (9.5%) | 13 (18%) | 16 (15%) | 8 (9.4%) |
| s_l_e | |||||
| FALSE | 188 (94%) | 122 (89%) | 47 (65%) | 73 (68%) | 79 (93%) |
| TRUE | 13 (6.5%) | 15 (11%) | 25 (35%) | 34 (32%) | 6 (7.1%) |
| 1 n (%) | |||||
chrom <- 17
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 151 (75%) | 55 (40%) | 13 (18%) | 35 (33%) | 27 (32%) |
| TRUE | 50 (25%) | 82 (60%) | 59 (82%) | 72 (67%) | 58 (68%) |
| b_e_e | |||||
| FALSE | 196 (98%) | 133 (97%) | 72 (100%) | 105 (98%) | 83 (98%) |
| TRUE | 5 (2.5%) | 4 (2.9%) | 0 (0%) | 2 (1.9%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 35 (17%) | 20 (15%) | 13 (18%) | 28 (26%) | 12 (14%) |
| TRUE | 166 (83%) | 117 (85%) | 59 (82%) | 79 (74%) | 73 (86%) |
| e_l_b | |||||
| FALSE | 55 (27%) | 86 (63%) | 59 (82%) | 74 (69%) | 60 (71%) |
| TRUE | 146 (73%) | 51 (37%) | 13 (18%) | 33 (31%) | 25 (29%) |
| e_l_s | |||||
| FALSE | 27 (13%) | 44 (32%) | 42 (58%) | 53 (50%) | 22 (26%) |
| TRUE | 174 (87%) | 93 (68%) | 30 (42%) | 54 (50%) | 63 (74%) |
| s_l_b | |||||
| FALSE | 168 (84%) | 118 (86%) | 60 (83%) | 80 (75%) | 73 (86%) |
| TRUE | 33 (16%) | 19 (14%) | 12 (17%) | 27 (25%) | 12 (14%) |
| s_l_e | |||||
| FALSE | 174 (87%) | 95 (69%) | 32 (44%) | 57 (53%) | 63 (74%) |
| TRUE | 27 (13%) | 42 (31%) | 40 (56%) | 50 (47%) | 22 (26%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 146 (73%) | 69 (50%) | 25 (35%) | 43 (40%) | 36 (42%) |
| TRUE | 55 (27%) | 68 (50%) | 47 (65%) | 64 (60%) | 49 (58%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 136 (99%) | 70 (97%) | 103 (96%) | 84 (99%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 2 (2.8%) | 4 (3.7%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 34 (17%) | 18 (13%) | 12 (17%) | 24 (22%) | 14 (16%) |
| TRUE | 167 (83%) | 119 (87%) | 60 (83%) | 83 (78%) | 71 (84%) |
| e_l_b | |||||
| FALSE | 56 (28%) | 69 (50%) | 49 (68%) | 68 (64%) | 50 (59%) |
| TRUE | 145 (72%) | 68 (50%) | 23 (32%) | 39 (36%) | 35 (41%) |
| e_l_s | |||||
| FALSE | 12 (6.0%) | 31 (23%) | 27 (38%) | 35 (33%) | 21 (25%) |
| TRUE | 189 (94%) | 106 (77%) | 45 (63%) | 72 (67%) | 64 (75%) |
| s_l_b | |||||
| FALSE | 172 (86%) | 120 (88%) | 61 (85%) | 84 (79%) | 71 (84%) |
| TRUE | 29 (14%) | 17 (12%) | 11 (15%) | 23 (21%) | 14 (16%) |
| s_l_e | |||||
| FALSE | 189 (94%) | 107 (78%) | 46 (64%) | 74 (69%) | 64 (75%) |
| TRUE | 12 (6.0%) | 30 (22%) | 26 (36%) | 33 (31%) | 21 (25%) |
| 1 n (%) | |||||
chrom <- 18
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 164 (82%) | 66 (48%) | 17 (24%) | 40 (37%) | 41 (48%) |
| TRUE | 37 (18%) | 71 (52%) | 55 (76%) | 67 (63%) | 44 (52%) |
| b_e_e | |||||
| FALSE | 197 (98%) | 133 (97%) | 71 (99%) | 104 (97%) | 82 (96%) |
| TRUE | 4 (2.0%) | 4 (2.9%) | 1 (1.4%) | 3 (2.8%) | 3 (3.5%) |
| b_l_s | |||||
| FALSE | 28 (14%) | 20 (15%) | 11 (15%) | 32 (30%) | 5 (5.9%) |
| TRUE | 173 (86%) | 117 (85%) | 61 (85%) | 75 (70%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 41 (20%) | 75 (55%) | 56 (78%) | 70 (65%) | 47 (55%) |
| TRUE | 160 (80%) | 62 (45%) | 16 (22%) | 37 (35%) | 38 (45%) |
| e_l_s | |||||
| FALSE | 11 (5.5%) | 25 (18%) | 28 (39%) | 47 (44%) | 18 (21%) |
| TRUE | 190 (95%) | 112 (82%) | 44 (61%) | 60 (56%) | 67 (79%) |
| s_l_b | |||||
| FALSE | 174 (87%) | 118 (86%) | 64 (89%) | 77 (72%) | 80 (94%) |
| TRUE | 27 (13%) | 19 (14%) | 8 (11%) | 30 (28%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 191 (95%) | 115 (84%) | 45 (63%) | 62 (58%) | 67 (79%) |
| TRUE | 10 (5.0%) | 22 (16%) | 27 (38%) | 45 (42%) | 18 (21%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 169 (84%) | 85 (62%) | 17 (24%) | 39 (36%) | 45 (53%) |
| TRUE | 32 (16%) | 52 (38%) | 55 (76%) | 68 (64%) | 40 (47%) |
| b_e_e | |||||
| FALSE | 199 (99%) | 134 (98%) | 71 (99%) | 104 (97%) | 83 (98%) |
| TRUE | 2 (1.0%) | 3 (2.2%) | 1 (1.4%) | 3 (2.8%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 20 (10.0%) | 12 (8.8%) | 12 (17%) | 23 (21%) | 7 (8.2%) |
| TRUE | 181 (90%) | 125 (91%) | 60 (83%) | 84 (79%) | 78 (92%) |
| e_l_b | |||||
| FALSE | 34 (17%) | 55 (40%) | 56 (78%) | 71 (66%) | 42 (49%) |
| TRUE | 167 (83%) | 82 (60%) | 16 (22%) | 36 (34%) | 43 (51%) |
| e_l_s | |||||
| FALSE | 6 (3.0%) | 21 (15%) | 27 (38%) | 31 (29%) | 13 (15%) |
| TRUE | 195 (97%) | 116 (85%) | 45 (63%) | 76 (71%) | 72 (85%) |
| s_l_b | |||||
| FALSE | 183 (91%) | 126 (92%) | 60 (83%) | 87 (81%) | 78 (92%) |
| TRUE | 18 (9.0%) | 11 (8.0%) | 12 (17%) | 20 (19%) | 7 (8.2%) |
| s_l_e | |||||
| FALSE | 195 (97%) | 116 (85%) | 46 (64%) | 76 (71%) | 72 (85%) |
| TRUE | 6 (3.0%) | 21 (15%) | 26 (36%) | 31 (29%) | 13 (15%) |
| 1 n (%) | |||||
chrom <- 19
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 107 (53%) | 44 (32%) | 24 (33%) | 32 (30%) | 36 (42%) |
| TRUE | 94 (47%) | 93 (68%) | 48 (67%) | 75 (70%) | 49 (58%) |
| b_e_e | |||||
| FALSE | 199 (99%) | 133 (97%) | 71 (99%) | 105 (98%) | 84 (99%) |
| TRUE | 2 (1.0%) | 4 (2.9%) | 1 (1.4%) | 2 (1.9%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 49 (24%) | 25 (18%) | 21 (29%) | 33 (31%) | 12 (14%) |
| TRUE | 152 (76%) | 112 (82%) | 51 (71%) | 74 (69%) | 73 (86%) |
| e_l_b | |||||
| FALSE | 96 (48%) | 97 (71%) | 49 (68%) | 77 (72%) | 50 (59%) |
| TRUE | 105 (52%) | 40 (29%) | 23 (32%) | 30 (28%) | 35 (41%) |
| e_l_s | |||||
| FALSE | 53 (26%) | 54 (39%) | 32 (44%) | 53 (50%) | 24 (28%) |
| TRUE | 148 (74%) | 83 (61%) | 40 (56%) | 54 (50%) | 61 (72%) |
| s_l_b | |||||
| FALSE | 155 (77%) | 113 (82%) | 52 (72%) | 78 (73%) | 73 (86%) |
| TRUE | 46 (23%) | 24 (18%) | 20 (28%) | 29 (27%) | 12 (14%) |
| s_l_e | |||||
| FALSE | 151 (75%) | 87 (64%) | 40 (56%) | 55 (51%) | 63 (74%) |
| TRUE | 50 (25%) | 50 (36%) | 32 (44%) | 52 (49%) | 22 (26%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 143 (71%) | 52 (38%) | 31 (43%) | 51 (48%) | 48 (56%) |
| TRUE | 58 (29%) | 85 (62%) | 41 (57%) | 56 (52%) | 37 (44%) |
| b_e_e | |||||
| FALSE | 199 (99%) | 134 (98%) | 72 (100%) | 106 (99%) | 84 (99%) |
| TRUE | 2 (1.0%) | 3 (2.2%) | 0 (0%) | 1 (0.9%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 42 (21%) | 24 (18%) | 20 (28%) | 36 (34%) | 9 (11%) |
| TRUE | 159 (79%) | 113 (82%) | 52 (72%) | 71 (66%) | 76 (89%) |
| e_l_b | |||||
| FALSE | 60 (30%) | 88 (64%) | 41 (57%) | 57 (53%) | 38 (45%) |
| TRUE | 141 (70%) | 49 (36%) | 31 (43%) | 50 (47%) | 47 (55%) |
| e_l_s | |||||
| FALSE | 32 (16%) | 41 (30%) | 26 (36%) | 43 (40%) | 6 (7.1%) |
| TRUE | 169 (84%) | 96 (70%) | 46 (64%) | 64 (60%) | 79 (93%) |
| s_l_b | |||||
| FALSE | 161 (80%) | 114 (83%) | 52 (72%) | 76 (71%) | 77 (91%) |
| TRUE | 40 (20%) | 23 (17%) | 20 (28%) | 31 (29%) | 8 (9.4%) |
| s_l_e | |||||
| FALSE | 174 (87%) | 99 (72%) | 46 (64%) | 65 (61%) | 79 (93%) |
| TRUE | 27 (13%) | 38 (28%) | 26 (36%) | 42 (39%) | 6 (7.1%) |
| 1 n (%) | |||||
chrom <- 20
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 141 (70%) | 59 (43%) | 22 (31%) | 34 (32%) | 39 (46%) |
| TRUE | 60 (30%) | 78 (57%) | 50 (69%) | 73 (68%) | 46 (54%) |
| b_e_e | |||||
| FALSE | 197 (98%) | 136 (99%) | 72 (100%) | 106 (99%) | 83 (98%) |
| TRUE | 4 (2.0%) | 1 (0.7%) | 0 (0%) | 1 (0.9%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 57 (28%) | 25 (18%) | 15 (21%) | 21 (20%) | 17 (20%) |
| TRUE | 144 (72%) | 112 (82%) | 57 (79%) | 86 (80%) | 68 (80%) |
| e_l_b | |||||
| FALSE | 64 (32%) | 79 (58%) | 50 (69%) | 74 (69%) | 48 (56%) |
| TRUE | 137 (68%) | 58 (42%) | 22 (31%) | 33 (31%) | 37 (44%) |
| e_l_s | |||||
| FALSE | 37 (18%) | 43 (31%) | 31 (43%) | 46 (43%) | 23 (27%) |
| TRUE | 164 (82%) | 94 (69%) | 41 (57%) | 61 (57%) | 62 (73%) |
| s_l_b | |||||
| FALSE | 148 (74%) | 115 (84%) | 59 (82%) | 88 (82%) | 69 (81%) |
| TRUE | 53 (26%) | 22 (16%) | 13 (18%) | 19 (18%) | 16 (19%) |
| s_l_e | |||||
| FALSE | 167 (83%) | 97 (71%) | 43 (60%) | 63 (59%) | 62 (73%) |
| TRUE | 34 (17%) | 40 (29%) | 29 (40%) | 44 (41%) | 23 (27%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 151 (75%) | 59 (43%) | 23 (32%) | 37 (35%) | 44 (52%) |
| TRUE | 50 (25%) | 78 (57%) | 49 (68%) | 70 (65%) | 41 (48%) |
| b_e_e | |||||
| FALSE | 197 (98%) | 134 (98%) | 71 (99%) | 103 (96%) | 85 (100%) |
| TRUE | 4 (2.0%) | 3 (2.2%) | 1 (1.4%) | 4 (3.7%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 49 (24%) | 22 (16%) | 16 (22%) | 31 (29%) | 16 (19%) |
| TRUE | 152 (76%) | 115 (84%) | 56 (78%) | 76 (71%) | 69 (81%) |
| e_l_b | |||||
| FALSE | 54 (27%) | 81 (59%) | 50 (69%) | 74 (69%) | 41 (48%) |
| TRUE | 147 (73%) | 56 (41%) | 22 (31%) | 33 (31%) | 44 (52%) |
| e_l_s | |||||
| FALSE | 27 (13%) | 33 (24%) | 27 (38%) | 43 (40%) | 18 (21%) |
| TRUE | 174 (87%) | 104 (76%) | 45 (63%) | 64 (60%) | 67 (79%) |
| s_l_b | |||||
| FALSE | 154 (77%) | 116 (85%) | 58 (81%) | 77 (72%) | 70 (82%) |
| TRUE | 47 (23%) | 21 (15%) | 14 (19%) | 30 (28%) | 15 (18%) |
| s_l_e | |||||
| FALSE | 180 (90%) | 105 (77%) | 46 (64%) | 64 (60%) | 68 (80%) |
| TRUE | 21 (10%) | 32 (23%) | 26 (36%) | 43 (40%) | 17 (20%) |
| 1 n (%) | |||||
chrom <- 21
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 112 (56%) | 44 (32%) | 19 (26%) | 35 (33%) | 33 (39%) |
| TRUE | 89 (44%) | 93 (68%) | 53 (74%) | 72 (67%) | 52 (61%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 133 (97%) | 71 (99%) | 102 (95%) | 81 (95%) |
| TRUE | 1 (0.5%) | 4 (2.9%) | 1 (1.4%) | 5 (4.7%) | 4 (4.7%) |
| b_l_s | |||||
| FALSE | 40 (20%) | 18 (13%) | 22 (31%) | 32 (30%) | 14 (16%) |
| TRUE | 161 (80%) | 119 (87%) | 50 (69%) | 75 (70%) | 71 (84%) |
| e_l_b | |||||
| FALSE | 90 (45%) | 97 (71%) | 54 (75%) | 77 (72%) | 56 (66%) |
| TRUE | 111 (55%) | 40 (29%) | 18 (25%) | 30 (28%) | 29 (34%) |
| e_l_s | |||||
| FALSE | 45 (22%) | 56 (41%) | 37 (51%) | 47 (44%) | 27 (32%) |
| TRUE | 156 (78%) | 81 (59%) | 35 (49%) | 60 (56%) | 58 (68%) |
| s_l_b | |||||
| FALSE | 166 (83%) | 122 (89%) | 51 (71%) | 79 (74%) | 71 (84%) |
| TRUE | 35 (17%) | 15 (11%) | 21 (29%) | 28 (26%) | 14 (16%) |
| s_l_e | |||||
| FALSE | 158 (79%) | 84 (61%) | 36 (50%) | 61 (57%) | 60 (71%) |
| TRUE | 43 (21%) | 53 (39%) | 36 (50%) | 46 (43%) | 25 (29%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 147 (73%) | 54 (39%) | 26 (36%) | 47 (44%) | 40 (47%) |
| TRUE | 54 (27%) | 83 (61%) | 46 (64%) | 60 (56%) | 45 (53%) |
| b_e_e | |||||
| FALSE | 196 (98%) | 133 (97%) | 72 (100%) | 103 (96%) | 83 (98%) |
| TRUE | 5 (2.5%) | 4 (2.9%) | 0 (0%) | 4 (3.7%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 33 (16%) | 26 (19%) | 19 (26%) | 20 (19%) | 13 (15%) |
| TRUE | 168 (84%) | 111 (81%) | 53 (74%) | 87 (81%) | 72 (85%) |
| e_l_b | |||||
| FALSE | 59 (29%) | 87 (64%) | 46 (64%) | 64 (60%) | 47 (55%) |
| TRUE | 142 (71%) | 50 (36%) | 26 (36%) | 43 (40%) | 38 (45%) |
| e_l_s | |||||
| FALSE | 23 (11%) | 41 (30%) | 32 (44%) | 44 (41%) | 20 (24%) |
| TRUE | 178 (89%) | 96 (70%) | 40 (56%) | 63 (59%) | 65 (76%) |
| s_l_b | |||||
| FALSE | 169 (84%) | 113 (82%) | 53 (74%) | 90 (84%) | 73 (86%) |
| TRUE | 32 (16%) | 24 (18%) | 19 (26%) | 17 (16%) | 12 (14%) |
| s_l_e | |||||
| FALSE | 180 (90%) | 99 (72%) | 41 (57%) | 68 (64%) | 66 (78%) |
| TRUE | 21 (10%) | 38 (28%) | 31 (43%) | 39 (36%) | 19 (22%) |
| 1 n (%) | |||||
chrom <- 22
plot_total_errors(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "Eagle", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_errors(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_errors, "SUPER", as.character(chrom))

cross_meth_plot({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "Total Errors", plot_total_errors_noth, "SUPER", as.character(chrom))

table_total_errors(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 113 (56%) | 35 (26%) | 15 (21%) | 33 (31%) | 28 (33%) |
| TRUE | 88 (44%) | 102 (74%) | 57 (79%) | 74 (69%) | 57 (67%) |
| b_e_e | |||||
| FALSE | 197 (98%) | 136 (99%) | 72 (100%) | 102 (95%) | 84 (99%) |
| TRUE | 4 (2.0%) | 1 (0.7%) | 0 (0%) | 5 (4.7%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 62 (31%) | 33 (24%) | 19 (26%) | 33 (31%) | 21 (25%) |
| TRUE | 139 (69%) | 104 (76%) | 53 (74%) | 74 (69%) | 64 (75%) |
| e_l_b | |||||
| FALSE | 92 (46%) | 103 (75%) | 57 (79%) | 79 (74%) | 58 (68%) |
| TRUE | 109 (54%) | 34 (25%) | 15 (21%) | 28 (26%) | 27 (32%) |
| e_l_s | |||||
| FALSE | 53 (26%) | 66 (48%) | 48 (67%) | 54 (50%) | 39 (46%) |
| TRUE | 148 (74%) | 71 (52%) | 24 (33%) | 53 (50%) | 46 (54%) |
| s_l_b | |||||
| FALSE | 143 (71%) | 108 (79%) | 54 (75%) | 76 (71%) | 64 (75%) |
| TRUE | 58 (29%) | 29 (21%) | 18 (25%) | 31 (29%) | 21 (25%) |
| s_l_e | |||||
| FALSE | 153 (76%) | 74 (54%) | 24 (33%) | 56 (52%) | 46 (54%) |
| TRUE | 48 (24%) | 63 (46%) | 48 (67%) | 51 (48%) | 39 (46%) |
| 1 n (%) | |||||
table_total_errors_noth({df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ]}, "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 118 (59%) | 53 (39%) | 20 (28%) | 48 (45%) | 36 (42%) |
| TRUE | 83 (41%) | 84 (61%) | 52 (72%) | 59 (55%) | 49 (58%) |
| b_e_e | |||||
| FALSE | 198 (99%) | 136 (99%) | 71 (99%) | 101 (94%) | 82 (96%) |
| TRUE | 3 (1.5%) | 1 (0.7%) | 1 (1.4%) | 6 (5.6%) | 3 (3.5%) |
| b_l_s | |||||
| FALSE | 58 (29%) | 29 (21%) | 21 (29%) | 29 (27%) | 12 (14%) |
| TRUE | 143 (71%) | 108 (79%) | 51 (71%) | 78 (73%) | 73 (86%) |
| e_l_b | |||||
| FALSE | 86 (43%) | 85 (62%) | 53 (74%) | 65 (61%) | 52 (61%) |
| TRUE | 115 (57%) | 52 (38%) | 19 (26%) | 42 (39%) | 33 (39%) |
| e_l_s | |||||
| FALSE | 61 (30%) | 49 (36%) | 38 (53%) | 49 (46%) | 23 (27%) |
| TRUE | 140 (70%) | 88 (64%) | 34 (47%) | 58 (54%) | 62 (73%) |
| s_l_b | |||||
| FALSE | 146 (73%) | 110 (80%) | 52 (72%) | 79 (74%) | 74 (87%) |
| TRUE | 55 (27%) | 27 (20%) | 20 (28%) | 28 (26%) | 11 (13%) |
| s_l_e | |||||
| FALSE | 144 (72%) | 90 (66%) | 34 (47%) | 62 (58%) | 66 (78%) |
| TRUE | 57 (28%) | 47 (34%) | 38 (53%) | 45 (42%) | 19 (22%) |
| 1 n (%) | |||||
plot_total_errors(df_switch_x, "Beagle", "Eagle", "pop", "X")

plot_total_errors(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

plot_total_errors(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

table_total_errors(df_switch_x, "pop")
| Characteristic | AFR N = 2001 |
AMR N = 2001 |
EAS N = 2001 |
EUR N = 2001 |
SAS N = 2001 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 1 (0.5%) | 6 (3.0%) | 1 (0.5%) | 0 (0%) | 1 (0.5%) |
| TRUE | 199 (100%) | 194 (97%) | 199 (100%) | 200 (100%) | 199 (100%) |
| b_e_e | |||||
| FALSE | 200 (100%) | 200 (100%) | 200 (100%) | 200 (100%) | 200 (100%) |
| b_l_s | |||||
| FALSE | 73 (37%) | 63 (32%) | 107 (54%) | 80 (40%) | 97 (49%) |
| TRUE | 127 (64%) | 137 (69%) | 93 (47%) | 120 (60%) | 103 (52%) |
| e_l_b | |||||
| FALSE | 199 (100%) | 194 (97%) | 199 (100%) | 200 (100%) | 199 (100%) |
| TRUE | 1 (0.5%) | 6 (3.0%) | 1 (0.5%) | 0 (0%) | 1 (0.5%) |
| e_l_s | |||||
| FALSE | 198 (99%) | 188 (94%) | 200 (100%) | 198 (99%) | 198 (99%) |
| TRUE | 2 (1.0%) | 12 (6.0%) | 0 (0%) | 2 (1.0%) | 2 (1.0%) |
| s_l_b | |||||
| FALSE | 135 (68%) | 141 (71%) | 101 (51%) | 127 (64%) | 103 (52%) |
| TRUE | 65 (33%) | 59 (30%) | 99 (50%) | 73 (37%) | 97 (49%) |
| s_l_e | |||||
| FALSE | 3 (1.5%) | 14 (7.0%) | 0 (0%) | 2 (1.0%) | 2 (1.0%) |
| TRUE | 197 (99%) | 186 (93%) | 200 (100%) | 198 (99%) | 198 (99%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_x, "Total Errors", plot_total_errors, "pop", "X")

plot_total_rate <- function(df, m1, m2, pop, chrom=as.character(chrom)){
p <- df %>%
mutate(Beagle = (n_other_beagle + n_flip_beagle) / n_hets,
Eagle = (n_other_eagle + n_flip_eagle) / n_hets,
SHAPEIT = (n_other_shapeit + n_flip_shapeit) / n_hets) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Error Rate", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
plot_total_rate_noth <- function(df, m1, m2, pop, chrom=as.character(chrom)){
p <- df %>%
mutate(Beagle = (n_switch_b + n_flip_b) / n_het,
Eagle = (n_switch_e + n_flip_e) / n_het,
SHAPEIT = (n_switch_s + n_flip_s) / n_het) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Error Rate", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
chrom <- 1
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 2
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 3
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 4
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 5
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 6
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 7
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 8
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 9
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 10
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 11
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 12
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 13
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 14
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 15
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 16
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 17
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 18
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 19
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 20
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 21
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

chrom <- 22
plot_total_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_total_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_total_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Total Errors", plot_total_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Total Errors", plot_total_rate_noth, "SUPER", as.character(chrom))

plot_total_rate(df_switch_x, "Beagle", "Eagle", "pop", "X")

plot_total_rate(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

plot_total_rate(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

cross_meth_plot(df_switch_x, "Total Errors", plot_total_rate, "pop", "X")

plot_switches <- function(df, m1, m2, pop, chrom=15){
p <- df %>%
mutate(Beagle = n_other_beagle,
Eagle = n_other_eagle,
SHAPEIT = n_other_shapeit) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Switches", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
plot_switches_noth <- function(df, m1, m2, pop, chrom=15){
p <- df %>%
mutate(Beagle = n_switch_b,
Eagle = n_switch_e,
SHAPEIT = n_switch_s) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Switches", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
table_switches <- function(df, pop){
res <- df %>%
mutate(Beagle = (n_other_beagle ),
Eagle = (n_other_eagle),
SHAPEIT = (n_other_shapeit)) %>%
mutate(b_l_e = factor(Beagle < Eagle),
b_l_s = factor(Beagle < SHAPEIT),
e_l_b = factor(Beagle > Eagle),
e_l_s = factor(Eagle < SHAPEIT),
s_l_b = factor(SHAPEIT < Beagle),
s_l_e = factor(SHAPEIT < Eagle)) %>%
tbl_summary(by = !! sym(pop),
include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
return(res)
}
table_switches_noth <- function(df, pop){
res <- df %>%
mutate(Beagle = (n_switch_b ),
Eagle = (n_switch_e),
SHAPEIT = (n_switch_s)) %>%
mutate(b_l_e = factor(Beagle < Eagle),
b_l_s = factor(Beagle < SHAPEIT),
e_l_b = factor(Beagle > Eagle),
e_l_s = factor(Eagle < SHAPEIT),
s_l_b = factor(SHAPEIT < Beagle),
s_l_e = factor(SHAPEIT < Eagle)) %>%
tbl_summary(by = !! sym(pop),
include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
return(res)
}
chrom <- 1
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 163 (81%) | 81 (59%) | 39 (54%) | 72 (67%) | 53 (62%) |
| TRUE | 38 (19%) | 56 (41%) | 33 (46%) | 35 (33%) | 32 (38%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 41 (20%) | 58 (42%) | 33 (46%) | 37 (35%) | 33 (39%) |
| TRUE | 160 (80%) | 79 (58%) | 39 (54%) | 70 (65%) | 52 (61%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 150 (75%) | 78 (57%) | 33 (46%) | 72 (67%) | 44 (52%) |
| TRUE | 51 (25%) | 59 (43%) | 39 (54%) | 35 (33%) | 41 (48%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 54 (27%) | 61 (45%) | 39 (54%) | 39 (36%) | 41 (48%) |
| TRUE | 147 (73%) | 76 (55%) | 33 (46%) | 68 (64%) | 44 (52%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 2
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 161 (80%) | 78 (57%) | 31 (43%) | 65 (61%) | 50 (59%) |
| TRUE | 40 (20%) | 59 (43%) | 41 (57%) | 42 (39%) | 35 (41%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 43 (21%) | 62 (45%) | 42 (58%) | 43 (40%) | 35 (41%) |
| TRUE | 158 (79%) | 75 (55%) | 30 (42%) | 64 (60%) | 50 (59%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 131 (65%) | 75 (55%) | 31 (43%) | 70 (65%) | 52 (61%) |
| TRUE | 70 (35%) | 62 (45%) | 41 (57%) | 37 (35%) | 33 (39%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 75 (37%) | 65 (47%) | 41 (57%) | 39 (36%) | 38 (45%) |
| TRUE | 126 (63%) | 72 (53%) | 31 (43%) | 68 (64%) | 47 (55%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 3
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 154 (77%) | 75 (55%) | 35 (49%) | 76 (71%) | 41 (48%) |
| TRUE | 47 (23%) | 62 (45%) | 37 (51%) | 31 (29%) | 44 (52%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 48 (24%) | 65 (47%) | 41 (57%) | 34 (32%) | 48 (56%) |
| TRUE | 153 (76%) | 72 (53%) | 31 (43%) | 73 (68%) | 37 (44%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 132 (66%) | 68 (50%) | 30 (42%) | 61 (57%) | 38 (45%) |
| TRUE | 69 (34%) | 69 (50%) | 42 (58%) | 46 (43%) | 47 (55%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 75 (37%) | 72 (53%) | 42 (58%) | 49 (46%) | 51 (60%) |
| TRUE | 126 (63%) | 65 (47%) | 30 (42%) | 58 (54%) | 34 (40%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 4
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 161 (80%) | 77 (56%) | 39 (54%) | 76 (71%) | 55 (65%) |
| TRUE | 40 (20%) | 60 (44%) | 33 (46%) | 31 (29%) | 30 (35%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 44 (22%) | 62 (45%) | 34 (47%) | 32 (30%) | 35 (41%) |
| TRUE | 157 (78%) | 75 (55%) | 38 (53%) | 75 (70%) | 50 (59%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 137 (68%) | 62 (45%) | 23 (32%) | 67 (63%) | 39 (46%) |
| TRUE | 64 (32%) | 75 (55%) | 49 (68%) | 40 (37%) | 46 (54%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 68 (34%) | 77 (56%) | 53 (74%) | 43 (40%) | 48 (56%) |
| TRUE | 133 (66%) | 60 (44%) | 19 (26%) | 64 (60%) | 37 (44%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 5
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 152 (76%) | 77 (56%) | 36 (50%) | 67 (63%) | 47 (55%) |
| TRUE | 49 (24%) | 60 (44%) | 36 (50%) | 40 (37%) | 38 (45%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 56 (28%) | 64 (47%) | 36 (50%) | 42 (39%) | 39 (46%) |
| TRUE | 145 (72%) | 73 (53%) | 36 (50%) | 65 (61%) | 46 (54%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 143 (71%) | 59 (43%) | 29 (40%) | 68 (64%) | 48 (56%) |
| TRUE | 58 (29%) | 78 (57%) | 43 (60%) | 39 (36%) | 37 (44%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 62 (31%) | 80 (58%) | 45 (63%) | 43 (40%) | 40 (47%) |
| TRUE | 139 (69%) | 57 (42%) | 27 (38%) | 64 (60%) | 45 (53%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 6
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 144 (72%) | 84 (61%) | 34 (47%) | 68 (64%) | 45 (53%) |
| TRUE | 57 (28%) | 53 (39%) | 38 (53%) | 39 (36%) | 40 (47%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 62 (31%) | 55 (40%) | 38 (53%) | 44 (41%) | 41 (48%) |
| TRUE | 139 (69%) | 82 (60%) | 34 (47%) | 63 (59%) | 44 (52%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 0 (0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 132 (66%) | 69 (50%) | 30 (42%) | 72 (67%) | 42 (49%) |
| TRUE | 69 (34%) | 68 (50%) | 42 (58%) | 35 (33%) | 43 (51%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 74 (37%) | 69 (50%) | 43 (60%) | 37 (35%) | 45 (53%) |
| TRUE | 127 (63%) | 68 (50%) | 29 (40%) | 70 (65%) | 40 (47%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 106 (99%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 7
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 84 (99%) |
| b_l_s | |||||
| FALSE | 172 (86%) | 74 (54%) | 31 (43%) | 79 (74%) | 47 (55%) |
| TRUE | 29 (14%) | 63 (46%) | 41 (57%) | 28 (26%) | 38 (45%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 84 (99%) |
| TRUE | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 84 (99%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| s_l_b | |||||
| FALSE | 29 (14%) | 63 (46%) | 42 (58%) | 36 (34%) | 39 (46%) |
| TRUE | 172 (86%) | 74 (54%) | 30 (42%) | 71 (66%) | 46 (54%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| TRUE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 84 (99%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 1 (0.5%) | 0 (0%) | 0 (0%) | 1 (0.9%) | 1 (1.2%) |
| TRUE | 200 (100%) | 137 (100%) | 72 (100%) | 106 (99%) | 84 (99%) |
| b_l_s | |||||
| FALSE | 149 (74%) | 76 (55%) | 34 (47%) | 73 (68%) | 46 (54%) |
| TRUE | 52 (26%) | 61 (45%) | 38 (53%) | 34 (32%) | 39 (46%) |
| e_l_b | |||||
| FALSE | 200 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 84 (99%) |
| TRUE | 1 (0.5%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 84 (99%) |
| TRUE | 0 (0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| s_l_b | |||||
| FALSE | 58 (29%) | 62 (45%) | 39 (54%) | 37 (35%) | 40 (47%) |
| TRUE | 143 (71%) | 75 (55%) | 33 (46%) | 70 (65%) | 45 (53%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| TRUE | 201 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 84 (99%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 8
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 175 (87%) | 105 (77%) | 63 (88%) | 90 (84%) | 63 (74%) |
| TRUE | 26 (13%) | 32 (23%) | 9 (13%) | 17 (16%) | 22 (26%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 31 (15%) | 35 (26%) | 10 (14%) | 23 (21%) | 25 (29%) |
| TRUE | 170 (85%) | 102 (74%) | 62 (86%) | 84 (79%) | 60 (71%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 2 (1.0%) | 1 (0.7%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 199 (99%) | 136 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 131 (65%) | 53 (39%) | 29 (40%) | 59 (55%) | 46 (54%) |
| TRUE | 70 (35%) | 84 (61%) | 43 (60%) | 48 (45%) | 39 (46%) |
| e_l_b | |||||
| FALSE | 199 (99%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 2 (1.0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 199 (99%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 2 (1.0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 76 (38%) | 87 (64%) | 45 (63%) | 50 (47%) | 43 (51%) |
| TRUE | 125 (62%) | 50 (36%) | 27 (38%) | 57 (53%) | 42 (49%) |
| s_l_e | |||||
| FALSE | 2 (1.0%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 199 (99%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 9
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 0 (0%) | 3 (2.2%) | 0 (0%) | 2 (1.9%) | 1 (1.2%) |
| TRUE | 201 (100%) | 134 (98%) | 72 (100%) | 105 (98%) | 84 (99%) |
| b_l_s | |||||
| FALSE | 165 (82%) | 92 (67%) | 42 (58%) | 79 (74%) | 58 (68%) |
| TRUE | 36 (18%) | 45 (33%) | 30 (42%) | 28 (26%) | 27 (32%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 135 (99%) | 72 (100%) | 105 (98%) | 84 (99%) |
| TRUE | 0 (0%) | 2 (1.5%) | 0 (0%) | 2 (1.9%) | 1 (1.2%) |
| e_l_s | |||||
| FALSE | 199 (99%) | 136 (99%) | 72 (100%) | 107 (100%) | 84 (99%) |
| TRUE | 2 (1.0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| s_l_b | |||||
| FALSE | 38 (19%) | 45 (33%) | 31 (43%) | 31 (29%) | 32 (38%) |
| TRUE | 163 (81%) | 92 (67%) | 41 (57%) | 76 (71%) | 53 (62%) |
| s_l_e | |||||
| FALSE | 2 (1.0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| TRUE | 199 (99%) | 136 (99%) | 72 (100%) | 107 (100%) | 84 (99%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 2 (1.0%) | 0 (0%) | 0 (0%) | 4 (3.7%) | 2 (2.4%) |
| TRUE | 199 (99%) | 137 (100%) | 72 (100%) | 103 (96%) | 83 (98%) |
| b_l_s | |||||
| FALSE | 151 (75%) | 72 (53%) | 39 (54%) | 73 (68%) | 50 (59%) |
| TRUE | 50 (25%) | 65 (47%) | 33 (46%) | 34 (32%) | 35 (41%) |
| e_l_b | |||||
| FALSE | 200 (100%) | 137 (100%) | 72 (100%) | 104 (97%) | 84 (99%) |
| TRUE | 1 (0.5%) | 0 (0%) | 0 (0%) | 3 (2.8%) | 1 (1.2%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 135 (99%) | 72 (100%) | 106 (99%) | 83 (98%) |
| TRUE | 1 (0.5%) | 2 (1.5%) | 0 (0%) | 1 (0.9%) | 2 (2.4%) |
| s_l_b | |||||
| FALSE | 56 (28%) | 68 (50%) | 36 (50%) | 39 (36%) | 36 (42%) |
| TRUE | 145 (72%) | 69 (50%) | 36 (50%) | 68 (64%) | 49 (58%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 2 (1.5%) | 0 (0%) | 1 (0.9%) | 2 (2.4%) |
| TRUE | 200 (100%) | 135 (99%) | 72 (100%) | 106 (99%) | 83 (98%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 10
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 152 (76%) | 79 (58%) | 37 (51%) | 79 (74%) | 51 (60%) |
| TRUE | 49 (24%) | 58 (42%) | 35 (49%) | 28 (26%) | 34 (40%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 53 (26%) | 59 (43%) | 35 (49%) | 30 (28%) | 37 (44%) |
| TRUE | 148 (74%) | 78 (57%) | 37 (51%) | 77 (72%) | 48 (56%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 153 (76%) | 84 (61%) | 33 (46%) | 78 (73%) | 47 (55%) |
| TRUE | 48 (24%) | 53 (39%) | 39 (54%) | 29 (27%) | 38 (45%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 53 (26%) | 58 (42%) | 40 (56%) | 32 (30%) | 40 (47%) |
| TRUE | 148 (74%) | 79 (58%) | 32 (44%) | 75 (70%) | 45 (53%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 11
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 144 (72%) | 78 (57%) | 39 (54%) | 68 (64%) | 50 (59%) |
| TRUE | 57 (28%) | 59 (43%) | 33 (46%) | 39 (36%) | 35 (41%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 62 (31%) | 61 (45%) | 35 (49%) | 44 (41%) | 36 (42%) |
| TRUE | 139 (69%) | 76 (55%) | 37 (51%) | 63 (59%) | 49 (58%) |
| s_l_e | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 3 (1.5%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 198 (99%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 131 (65%) | 68 (50%) | 37 (51%) | 69 (64%) | 52 (61%) |
| TRUE | 70 (35%) | 69 (50%) | 35 (49%) | 38 (36%) | 33 (39%) |
| e_l_b | |||||
| FALSE | 198 (99%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 3 (1.5%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 1 (0.5%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 75 (37%) | 74 (54%) | 37 (51%) | 39 (36%) | 37 (44%) |
| TRUE | 126 (63%) | 63 (46%) | 35 (49%) | 68 (64%) | 48 (56%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 200 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 12
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 1 (0.5%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| TRUE | 200 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 84 (99%) |
| b_l_s | |||||
| FALSE | 147 (73%) | 79 (58%) | 35 (49%) | 71 (66%) | 44 (52%) |
| TRUE | 54 (27%) | 58 (42%) | 37 (51%) | 36 (34%) | 41 (48%) |
| e_l_b | |||||
| FALSE | 200 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 84 (99%) |
| TRUE | 1 (0.5%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 84 (99%) |
| TRUE | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| s_l_b | |||||
| FALSE | 58 (29%) | 61 (45%) | 39 (54%) | 40 (37%) | 43 (51%) |
| TRUE | 143 (71%) | 76 (55%) | 33 (46%) | 67 (63%) | 42 (49%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| TRUE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 84 (99%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 84 (99%) |
| b_l_s | |||||
| FALSE | 143 (71%) | 69 (50%) | 33 (46%) | 65 (61%) | 45 (53%) |
| TRUE | 58 (29%) | 68 (50%) | 39 (54%) | 42 (39%) | 40 (47%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 84 (99%) |
| TRUE | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 137 (100%) | 72 (100%) | 106 (99%) | 84 (99%) |
| TRUE | 1 (0.5%) | 0 (0%) | 0 (0%) | 1 (0.9%) | 1 (1.2%) |
| s_l_b | |||||
| FALSE | 61 (30%) | 72 (53%) | 42 (58%) | 45 (42%) | 42 (49%) |
| TRUE | 140 (70%) | 65 (47%) | 30 (42%) | 62 (58%) | 43 (51%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 2 (1.5%) | 0 (0%) | 1 (0.9%) | 1 (1.2%) |
| TRUE | 200 (100%) | 135 (99%) | 72 (100%) | 106 (99%) | 84 (99%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 13
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 1 (0.5%) | 1 (0.7%) | 1 (1.4%) | 2 (1.9%) | 1 (1.2%) |
| TRUE | 200 (100%) | 136 (99%) | 71 (99%) | 105 (98%) | 84 (99%) |
| b_l_s | |||||
| FALSE | 148 (74%) | 80 (58%) | 41 (57%) | 68 (64%) | 50 (59%) |
| TRUE | 53 (26%) | 57 (42%) | 31 (43%) | 39 (36%) | 35 (41%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 136 (99%) | 71 (99%) | 105 (98%) | 84 (99%) |
| TRUE | 0 (0%) | 1 (0.7%) | 1 (1.4%) | 2 (1.9%) | 1 (1.2%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 84 (99%) |
| TRUE | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| s_l_b | |||||
| FALSE | 62 (31%) | 63 (46%) | 31 (43%) | 40 (37%) | 39 (46%) |
| TRUE | 139 (69%) | 74 (54%) | 41 (57%) | 67 (63%) | 46 (54%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 0 (0%) | 0 (0%) | 0 (0%) | 1 (1.2%) |
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 84 (99%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 2 (1.9%) | 1 (1.2%) |
| TRUE | 200 (100%) | 136 (99%) | 72 (100%) | 105 (98%) | 84 (99%) |
| b_l_s | |||||
| FALSE | 128 (64%) | 61 (45%) | 35 (49%) | 65 (61%) | 42 (49%) |
| TRUE | 73 (36%) | 76 (55%) | 37 (51%) | 42 (39%) | 43 (51%) |
| e_l_b | |||||
| FALSE | 200 (100%) | 136 (99%) | 72 (100%) | 105 (98%) | 84 (99%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 2 (1.9%) | 1 (1.2%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 135 (99%) | 72 (100%) | 105 (98%) | 85 (100%) |
| TRUE | 1 (0.5%) | 2 (1.5%) | 0 (0%) | 2 (1.9%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 81 (40%) | 82 (60%) | 39 (54%) | 45 (42%) | 48 (56%) |
| TRUE | 120 (60%) | 55 (40%) | 33 (46%) | 62 (58%) | 37 (44%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 2 (1.5%) | 0 (0%) | 2 (1.9%) | 0 (0%) |
| TRUE | 200 (100%) | 135 (99%) | 72 (100%) | 105 (98%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 14
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 200 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 146 (73%) | 67 (49%) | 38 (53%) | 65 (61%) | 45 (53%) |
| TRUE | 55 (27%) | 70 (51%) | 34 (47%) | 42 (39%) | 40 (47%) |
| e_l_b | |||||
| FALSE | 200 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 135 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 1 (0.5%) | 2 (1.5%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 61 (30%) | 75 (55%) | 37 (51%) | 46 (43%) | 41 (48%) |
| TRUE | 140 (70%) | 62 (45%) | 35 (49%) | 61 (57%) | 44 (52%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 2 (1.5%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 200 (100%) | 135 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 2 (1.0%) | 1 (0.7%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 199 (99%) | 136 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 127 (63%) | 68 (50%) | 37 (51%) | 64 (60%) | 41 (48%) |
| TRUE | 74 (37%) | 69 (50%) | 35 (49%) | 43 (40%) | 44 (52%) |
| e_l_b | |||||
| FALSE | 199 (99%) | 137 (100%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 2 (1.0%) | 0 (0%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 137 (100%) | 71 (99%) | 106 (99%) | 84 (99%) |
| TRUE | 1 (0.5%) | 0 (0%) | 1 (1.4%) | 1 (0.9%) | 1 (1.2%) |
| s_l_b | |||||
| FALSE | 80 (40%) | 74 (54%) | 41 (57%) | 45 (42%) | 46 (54%) |
| TRUE | 121 (60%) | 63 (46%) | 31 (43%) | 62 (58%) | 39 (46%) |
| s_l_e | |||||
| FALSE | 3 (1.5%) | 0 (0%) | 1 (1.4%) | 1 (0.9%) | 2 (2.4%) |
| TRUE | 198 (99%) | 137 (100%) | 71 (99%) | 106 (99%) | 83 (98%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 15
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 6 (3.0%) | 2 (1.5%) | 0 (0%) | 2 (1.9%) | 1 (1.2%) |
| TRUE | 195 (97%) | 135 (99%) | 72 (100%) | 105 (98%) | 84 (99%) |
| b_l_s | |||||
| FALSE | 138 (69%) | 77 (56%) | 41 (57%) | 74 (69%) | 53 (62%) |
| TRUE | 63 (31%) | 60 (44%) | 31 (43%) | 33 (31%) | 32 (38%) |
| e_l_b | |||||
| FALSE | 196 (98%) | 136 (99%) | 72 (100%) | 105 (98%) | 84 (99%) |
| TRUE | 5 (2.5%) | 1 (0.7%) | 0 (0%) | 2 (1.9%) | 1 (1.2%) |
| e_l_s | |||||
| FALSE | 199 (99%) | 133 (97%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 2 (1.0%) | 4 (2.9%) | 0 (0%) | 0 (0%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 64 (32%) | 64 (47%) | 31 (43%) | 39 (36%) | 36 (42%) |
| TRUE | 137 (68%) | 73 (53%) | 41 (57%) | 68 (64%) | 49 (58%) |
| s_l_e | |||||
| FALSE | 2 (1.0%) | 4 (2.9%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 199 (99%) | 133 (97%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 4 (2.0%) | 2 (1.5%) | 1 (1.4%) | 2 (1.9%) | 0 (0%) |
| TRUE | 197 (98%) | 135 (99%) | 71 (99%) | 105 (98%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 138 (69%) | 69 (50%) | 34 (47%) | 70 (65%) | 37 (44%) |
| TRUE | 63 (31%) | 68 (50%) | 38 (53%) | 37 (35%) | 48 (56%) |
| e_l_b | |||||
| FALSE | 197 (98%) | 135 (99%) | 71 (99%) | 106 (99%) | 85 (100%) |
| TRUE | 4 (2.0%) | 2 (1.5%) | 1 (1.4%) | 1 (0.9%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 136 (99%) | 72 (100%) | 106 (99%) | 83 (98%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 1 (0.9%) | 2 (2.4%) |
| s_l_b | |||||
| FALSE | 68 (34%) | 73 (53%) | 38 (53%) | 42 (39%) | 51 (60%) |
| TRUE | 133 (66%) | 64 (47%) | 34 (47%) | 65 (61%) | 34 (40%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 1 (0.7%) | 1 (1.4%) | 1 (0.9%) | 2 (2.4%) |
| TRUE | 200 (100%) | 136 (99%) | 71 (99%) | 106 (99%) | 83 (98%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 16
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 200 (100%) | 136 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 150 (75%) | 76 (55%) | 47 (65%) | 70 (65%) | 51 (60%) |
| TRUE | 51 (25%) | 61 (45%) | 25 (35%) | 37 (35%) | 34 (40%) |
| e_l_b | |||||
| FALSE | 200 (100%) | 137 (100%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 1 (0.5%) | 0 (0%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 55 (27%) | 62 (45%) | 27 (38%) | 41 (38%) | 39 (46%) |
| TRUE | 146 (73%) | 75 (55%) | 45 (63%) | 66 (62%) | 46 (54%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 0 (0%) | 0 (0%) | 2 (1.9%) | 0 (0%) |
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 105 (98%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 1 (0.5%) | 0 (0%) | 1 (1.4%) | 0 (0%) | 3 (3.5%) |
| TRUE | 200 (100%) | 137 (100%) | 71 (99%) | 107 (100%) | 82 (96%) |
| b_l_s | |||||
| FALSE | 146 (73%) | 67 (49%) | 27 (38%) | 51 (48%) | 39 (46%) |
| TRUE | 55 (27%) | 70 (51%) | 45 (63%) | 56 (52%) | 46 (54%) |
| e_l_b | |||||
| FALSE | 200 (100%) | 137 (100%) | 71 (99%) | 107 (100%) | 82 (96%) |
| TRUE | 1 (0.5%) | 0 (0%) | 1 (1.4%) | 0 (0%) | 3 (3.5%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 80 (94%) |
| TRUE | 1 (0.5%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 5 (5.9%) |
| s_l_b | |||||
| FALSE | 59 (29%) | 74 (54%) | 46 (64%) | 57 (53%) | 47 (55%) |
| TRUE | 142 (71%) | 63 (46%) | 26 (36%) | 50 (47%) | 38 (45%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 3 (2.2%) | 0 (0%) | 0 (0%) | 6 (7.1%) |
| TRUE | 200 (100%) | 134 (98%) | 72 (100%) | 107 (100%) | 79 (93%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 17
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 0 (0%) | 4 (2.9%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 201 (100%) | 133 (97%) | 72 (100%) | 106 (99%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 156 (78%) | 99 (72%) | 41 (57%) | 77 (72%) | 52 (61%) |
| TRUE | 45 (22%) | 38 (28%) | 31 (43%) | 30 (28%) | 33 (39%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 134 (98%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 136 (99%) | 71 (99%) | 107 (100%) | 85 (100%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 1 (1.4%) | 0 (0%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 48 (24%) | 44 (32%) | 34 (47%) | 36 (34%) | 35 (41%) |
| TRUE | 153 (76%) | 93 (68%) | 38 (53%) | 71 (66%) | 50 (59%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 1 (0.7%) | 1 (1.4%) | 0 (0%) | 0 (0%) |
| TRUE | 200 (100%) | 136 (99%) | 71 (99%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 200 (100%) | 136 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 133 (66%) | 85 (62%) | 32 (44%) | 67 (63%) | 56 (66%) |
| TRUE | 68 (34%) | 52 (38%) | 40 (56%) | 40 (37%) | 29 (34%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 199 (99%) | 136 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 2 (1.0%) | 1 (0.7%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 71 (35%) | 61 (45%) | 43 (60%) | 43 (40%) | 31 (36%) |
| TRUE | 130 (65%) | 76 (55%) | 29 (40%) | 64 (60%) | 54 (64%) |
| s_l_e | |||||
| FALSE | 2 (1.0%) | 1 (0.7%) | 0 (0%) | 1 (0.9%) | 1 (1.2%) |
| TRUE | 199 (99%) | 136 (99%) | 72 (100%) | 106 (99%) | 84 (99%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 18
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 2 (1.0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 199 (99%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 139 (69%) | 74 (54%) | 37 (51%) | 60 (56%) | 50 (59%) |
| TRUE | 62 (31%) | 63 (46%) | 35 (49%) | 47 (44%) | 35 (41%) |
| e_l_b | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 136 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 1 (0.5%) | 1 (0.7%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 65 (32%) | 66 (48%) | 40 (56%) | 53 (50%) | 38 (45%) |
| TRUE | 136 (68%) | 71 (52%) | 32 (44%) | 54 (50%) | 47 (55%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 2 (1.5%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 200 (100%) | 135 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 4 (2.0%) | 5 (3.6%) | 0 (0%) | 3 (2.8%) | 1 (1.2%) |
| TRUE | 197 (98%) | 132 (96%) | 72 (100%) | 104 (97%) | 84 (99%) |
| b_l_s | |||||
| FALSE | 130 (65%) | 72 (53%) | 36 (50%) | 56 (52%) | 50 (59%) |
| TRUE | 71 (35%) | 65 (47%) | 36 (50%) | 51 (48%) | 35 (41%) |
| e_l_b | |||||
| FALSE | 197 (98%) | 134 (98%) | 72 (100%) | 104 (97%) | 84 (99%) |
| TRUE | 4 (2.0%) | 3 (2.2%) | 0 (0%) | 3 (2.8%) | 1 (1.2%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 130 (95%) | 70 (97%) | 106 (99%) | 85 (100%) |
| TRUE | 1 (0.5%) | 7 (5.1%) | 2 (2.8%) | 1 (0.9%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 79 (39%) | 70 (51%) | 37 (51%) | 57 (53%) | 38 (45%) |
| TRUE | 122 (61%) | 67 (49%) | 35 (49%) | 50 (47%) | 47 (55%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 7 (5.1%) | 2 (2.8%) | 2 (1.9%) | 0 (0%) |
| TRUE | 200 (100%) | 130 (95%) | 70 (97%) | 105 (98%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 19
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 2 (1.0%) | 1 (0.7%) | 1 (1.4%) | 0 (0%) | 4 (4.7%) |
| TRUE | 199 (99%) | 136 (99%) | 71 (99%) | 107 (100%) | 81 (95%) |
| b_l_s | |||||
| FALSE | 153 (76%) | 89 (65%) | 40 (56%) | 60 (56%) | 60 (71%) |
| TRUE | 48 (24%) | 48 (35%) | 32 (44%) | 47 (44%) | 25 (29%) |
| e_l_b | |||||
| FALSE | 199 (99%) | 136 (99%) | 72 (100%) | 107 (100%) | 82 (96%) |
| TRUE | 2 (1.0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 3 (3.5%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 82 (96%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 3 (3.5%) |
| s_l_b | |||||
| FALSE | 55 (27%) | 51 (37%) | 32 (44%) | 50 (47%) | 28 (33%) |
| TRUE | 146 (73%) | 86 (63%) | 40 (56%) | 57 (53%) | 57 (67%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 3 (3.5%) |
| TRUE | 201 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 82 (96%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 4 (2.0%) | 8 (5.8%) | 1 (1.4%) | 3 (2.8%) | 0 (0%) |
| TRUE | 197 (98%) | 129 (94%) | 71 (99%) | 104 (97%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 139 (69%) | 83 (61%) | 37 (51%) | 67 (63%) | 47 (55%) |
| TRUE | 62 (31%) | 54 (39%) | 35 (49%) | 40 (37%) | 38 (45%) |
| e_l_b | |||||
| FALSE | 197 (98%) | 130 (95%) | 72 (100%) | 104 (97%) | 85 (100%) |
| TRUE | 4 (2.0%) | 7 (5.1%) | 0 (0%) | 3 (2.8%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 132 (96%) | 70 (97%) | 107 (100%) | 80 (94%) |
| TRUE | 0 (0%) | 5 (3.6%) | 2 (2.8%) | 0 (0%) | 5 (5.9%) |
| s_l_b | |||||
| FALSE | 70 (35%) | 57 (42%) | 37 (51%) | 46 (43%) | 38 (45%) |
| TRUE | 131 (65%) | 80 (58%) | 35 (49%) | 61 (57%) | 47 (55%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 5 (3.6%) | 2 (2.8%) | 1 (0.9%) | 6 (7.1%) |
| TRUE | 201 (100%) | 132 (96%) | 70 (97%) | 106 (99%) | 79 (93%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 20
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 3 (1.5%) | 2 (1.5%) | 2 (2.8%) | 3 (2.8%) | 0 (0%) |
| TRUE | 198 (99%) | 135 (99%) | 70 (97%) | 104 (97%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 164 (82%) | 78 (57%) | 44 (61%) | 76 (71%) | 54 (64%) |
| TRUE | 37 (18%) | 59 (43%) | 28 (39%) | 31 (29%) | 31 (36%) |
| e_l_b | |||||
| FALSE | 199 (99%) | 137 (100%) | 70 (97%) | 104 (97%) | 85 (100%) |
| TRUE | 2 (1.0%) | 0 (0%) | 2 (2.8%) | 3 (2.8%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 201 (100%) | 134 (98%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| s_l_b | |||||
| FALSE | 40 (20%) | 63 (46%) | 31 (43%) | 35 (33%) | 34 (40%) |
| TRUE | 161 (80%) | 74 (54%) | 41 (57%) | 72 (67%) | 51 (60%) |
| s_l_e | |||||
| FALSE | 0 (0%) | 3 (2.2%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 201 (100%) | 134 (98%) | 72 (100%) | 106 (99%) | 85 (100%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 4 (2.0%) | 5 (3.6%) | 2 (2.8%) | 4 (3.7%) | 0 (0%) |
| TRUE | 197 (98%) | 132 (96%) | 70 (97%) | 103 (96%) | 85 (100%) |
| b_l_s | |||||
| FALSE | 145 (72%) | 77 (56%) | 40 (56%) | 67 (63%) | 52 (61%) |
| TRUE | 56 (28%) | 60 (44%) | 32 (44%) | 40 (37%) | 33 (39%) |
| e_l_b | |||||
| FALSE | 199 (99%) | 134 (98%) | 70 (97%) | 103 (96%) | 85 (100%) |
| TRUE | 2 (1.0%) | 3 (2.2%) | 2 (2.8%) | 4 (3.7%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 135 (99%) | 71 (99%) | 107 (100%) | 84 (99%) |
| TRUE | 1 (0.5%) | 2 (1.5%) | 1 (1.4%) | 0 (0%) | 1 (1.2%) |
| s_l_b | |||||
| FALSE | 59 (29%) | 63 (46%) | 32 (44%) | 42 (39%) | 34 (40%) |
| TRUE | 142 (71%) | 74 (54%) | 40 (56%) | 65 (61%) | 51 (60%) |
| s_l_e | |||||
| FALSE | 1 (0.5%) | 2 (1.5%) | 1 (1.4%) | 0 (0%) | 1 (1.2%) |
| TRUE | 200 (100%) | 135 (99%) | 71 (99%) | 107 (100%) | 84 (99%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 21
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 7 (3.5%) | 12 (8.8%) | 6 (8.3%) | 14 (13%) | 6 (7.1%) |
| TRUE | 194 (97%) | 125 (91%) | 66 (92%) | 93 (87%) | 79 (93%) |
| b_l_s | |||||
| FALSE | 125 (62%) | 69 (50%) | 39 (54%) | 67 (63%) | 48 (56%) |
| TRUE | 76 (38%) | 68 (50%) | 33 (46%) | 40 (37%) | 37 (44%) |
| e_l_b | |||||
| FALSE | 196 (98%) | 127 (93%) | 67 (93%) | 98 (92%) | 81 (95%) |
| TRUE | 5 (2.5%) | 10 (7.3%) | 5 (6.9%) | 9 (8.4%) | 4 (4.7%) |
| e_l_s | |||||
| FALSE | 197 (98%) | 123 (90%) | 69 (96%) | 99 (93%) | 84 (99%) |
| TRUE | 4 (2.0%) | 14 (10%) | 3 (4.2%) | 8 (7.5%) | 1 (1.2%) |
| s_l_b | |||||
| FALSE | 80 (40%) | 73 (53%) | 35 (49%) | 45 (42%) | 37 (44%) |
| TRUE | 121 (60%) | 64 (47%) | 37 (51%) | 62 (58%) | 48 (56%) |
| s_l_e | |||||
| FALSE | 5 (2.5%) | 15 (11%) | 3 (4.2%) | 10 (9.3%) | 2 (2.4%) |
| TRUE | 196 (98%) | 122 (89%) | 69 (96%) | 97 (91%) | 83 (98%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 13 (6.5%) | 15 (11%) | 5 (6.9%) | 18 (17%) | 5 (5.9%) |
| TRUE | 188 (94%) | 122 (89%) | 67 (93%) | 89 (83%) | 80 (94%) |
| b_l_s | |||||
| FALSE | 122 (61%) | 69 (50%) | 40 (56%) | 56 (52%) | 37 (44%) |
| TRUE | 79 (39%) | 68 (50%) | 32 (44%) | 51 (48%) | 48 (56%) |
| e_l_b | |||||
| FALSE | 192 (96%) | 125 (91%) | 68 (94%) | 89 (83%) | 80 (94%) |
| TRUE | 9 (4.5%) | 12 (8.8%) | 4 (5.6%) | 18 (17%) | 5 (5.9%) |
| e_l_s | |||||
| FALSE | 191 (95%) | 119 (87%) | 69 (96%) | 101 (94%) | 82 (96%) |
| TRUE | 10 (5.0%) | 18 (13%) | 3 (4.2%) | 6 (5.6%) | 3 (3.5%) |
| s_l_b | |||||
| FALSE | 91 (45%) | 77 (56%) | 36 (50%) | 54 (50%) | 51 (60%) |
| TRUE | 110 (55%) | 60 (44%) | 36 (50%) | 53 (50%) | 34 (40%) |
| s_l_e | |||||
| FALSE | 14 (7.0%) | 20 (15%) | 3 (4.2%) | 9 (8.4%) | 3 (3.5%) |
| TRUE | 187 (93%) | 117 (85%) | 69 (96%) | 98 (92%) | 82 (96%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

chrom <- 22
plot_switches(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switches(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_switches(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 9 (4.5%) | 5 (3.6%) | 3 (4.2%) | 6 (5.6%) | 4 (4.7%) |
| TRUE | 192 (96%) | 132 (96%) | 69 (96%) | 101 (94%) | 81 (95%) |
| b_l_s | |||||
| FALSE | 153 (76%) | 82 (60%) | 42 (58%) | 73 (68%) | 57 (67%) |
| TRUE | 48 (24%) | 55 (40%) | 30 (42%) | 34 (32%) | 28 (33%) |
| e_l_b | |||||
| FALSE | 195 (97%) | 132 (96%) | 70 (97%) | 101 (94%) | 81 (95%) |
| TRUE | 6 (3.0%) | 5 (3.6%) | 2 (2.8%) | 6 (5.6%) | 4 (4.7%) |
| e_l_s | |||||
| FALSE | 198 (99%) | 133 (97%) | 70 (97%) | 106 (99%) | 83 (98%) |
| TRUE | 3 (1.5%) | 4 (2.9%) | 2 (2.8%) | 1 (0.9%) | 2 (2.4%) |
| s_l_b | |||||
| FALSE | 57 (28%) | 59 (43%) | 32 (44%) | 36 (34%) | 30 (35%) |
| TRUE | 144 (72%) | 78 (57%) | 40 (56%) | 71 (66%) | 55 (65%) |
| s_l_e | |||||
| FALSE | 4 (2.0%) | 5 (3.6%) | 2 (2.8%) | 3 (2.8%) | 3 (3.5%) |
| TRUE | 197 (98%) | 132 (96%) | 70 (97%) | 104 (97%) | 82 (96%) |
| 1 n (%) | |||||
table_switches_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 10 (5.0%) | 13 (9.5%) | 4 (5.6%) | 16 (15%) | 10 (12%) |
| TRUE | 191 (95%) | 124 (91%) | 68 (94%) | 91 (85%) | 75 (88%) |
| b_l_s | |||||
| FALSE | 149 (74%) | 79 (58%) | 41 (57%) | 57 (53%) | 53 (62%) |
| TRUE | 52 (26%) | 58 (42%) | 31 (43%) | 50 (47%) | 32 (38%) |
| e_l_b | |||||
| FALSE | 195 (97%) | 126 (92%) | 68 (94%) | 94 (88%) | 76 (89%) |
| TRUE | 6 (3.0%) | 11 (8.0%) | 4 (5.6%) | 13 (12%) | 9 (11%) |
| e_l_s | |||||
| FALSE | 198 (99%) | 130 (95%) | 68 (94%) | 94 (88%) | 76 (89%) |
| TRUE | 3 (1.5%) | 7 (5.1%) | 4 (5.6%) | 13 (12%) | 9 (11%) |
| s_l_b | |||||
| FALSE | 56 (28%) | 65 (47%) | 34 (47%) | 54 (50%) | 33 (39%) |
| TRUE | 145 (72%) | 72 (53%) | 38 (53%) | 53 (50%) | 52 (61%) |
| s_l_e | |||||
| FALSE | 3 (1.5%) | 7 (5.1%) | 4 (5.6%) | 14 (13%) | 9 (11%) |
| TRUE | 198 (99%) | 130 (95%) | 68 (94%) | 93 (87%) | 76 (89%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switches, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switches_noth, "SUPER", as.character(chrom))

plot_switches(df_switch_x, "Beagle", "Eagle", "pop", "X")

plot_switches(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

plot_switches(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

table_switches(df_switch_x, "pop")
| Characteristic | AFR N = 2001 |
AMR N = 2001 |
EAS N = 2001 |
EUR N = 2001 |
SAS N = 2001 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 0 (0%) | 0 (0%) | 1 (0.5%) | 0 (0%) | 0 (0%) |
| TRUE | 200 (100%) | 200 (100%) | 199 (100%) | 200 (100%) | 200 (100%) |
| b_l_s | |||||
| FALSE | 174 (87%) | 150 (75%) | 163 (82%) | 162 (81%) | 166 (83%) |
| TRUE | 26 (13%) | 50 (25%) | 37 (19%) | 38 (19%) | 34 (17%) |
| e_l_b | |||||
| FALSE | 200 (100%) | 200 (100%) | 199 (100%) | 200 (100%) | 200 (100%) |
| TRUE | 0 (0%) | 0 (0%) | 1 (0.5%) | 0 (0%) | 0 (0%) |
| e_l_s | |||||
| FALSE | 200 (100%) | 200 (100%) | 200 (100%) | 200 (100%) | 200 (100%) |
| s_l_b | |||||
| FALSE | 30 (15%) | 58 (29%) | 45 (23%) | 49 (25%) | 39 (20%) |
| TRUE | 170 (85%) | 142 (71%) | 155 (78%) | 151 (76%) | 161 (81%) |
| s_l_e | |||||
| TRUE | 200 (100%) | 200 (100%) | 200 (100%) | 200 (100%) | 200 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_x, "Switches", plot_switches, "pop", "X")

plot_switch_rate <- function(df, m1, m2, pop, chrom = 15){
p <- df %>%
mutate(Beagle = n_other_beagle / n_hets,
Eagle = n_other_eagle / n_hets,
SHAPEIT = n_other_shapeit / n_hets) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Switch Rate", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
plot_switch_rate_noth <- function(df, m1, m2, pop, chrom = 15){
p <- df %>%
mutate(Beagle = n_switch_b / n_het,
Eagle = n_switch_e / n_het,
SHAPEIT = n_switch_s / n_het) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Switch Rate", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
chrom <- 1
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 2
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 3
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 4
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 5
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 6
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 7
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 8
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 9
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 10
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 11
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 12
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 13
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 14
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 15
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 16
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 17
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 18
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 19
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 20
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 21
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

chrom <- 22
plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_switch_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_switch_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Switches", plot_switch_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Switches", plot_switch_rate_noth, "SUPER", as.character(chrom))

plot_switch_rate(df_switch_x, "Beagle", "Eagle", "pop", "X")

plot_switch_rate(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

plot_switch_rate(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

cross_meth_plot(df_switch_x, "Switches", plot_switch_rate, "pop", "X")

plot_flips <- function(df, m1, m2, pop, chrom = 15){
p <- df %>%
mutate(Beagle = n_flip_beagle,
Eagle = n_flip_eagle,
SHAPEIT = n_flip_shapeit) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Total Flips", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
plot_flips_noth <- function(df, m1, m2, pop, chrom = 15){
p <- df %>%
mutate(Beagle = n_flip_b,
Eagle = n_flip_e,
SHAPEIT = n_flip_s) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Total Flips", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
table_flip <- function(df, pop){
res <- df %>%
mutate(Beagle = (n_flip_beagle ),
Eagle = (n_flip_eagle),
SHAPEIT = (n_flip_shapeit)) %>%
mutate(b_l_e = factor(Beagle < Eagle),
b_l_s = factor(Beagle < SHAPEIT),
e_l_b = factor(Beagle > Eagle),
e_l_s = factor(Eagle < SHAPEIT),
s_l_b = factor(SHAPEIT < Beagle),
s_l_e = factor(SHAPEIT < Eagle)) %>%
tbl_summary(by = !! sym(pop),
include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
return(res)
}
table_flip_noth <- function(df, pop){
res <- df %>%
mutate(Beagle = (n_flip_b ),
Eagle = (n_flip_e),
SHAPEIT = (n_flip_s)) %>%
mutate(b_l_e = factor(Beagle < Eagle),
b_l_s = factor(Beagle < SHAPEIT),
e_l_b = factor(Beagle > Eagle),
e_l_s = factor(Eagle < SHAPEIT),
s_l_b = factor(SHAPEIT < Beagle),
s_l_e = factor(SHAPEIT < Eagle)) %>%
tbl_summary(by = !! sym(pop),
include = c(b_l_e, b_l_s, e_l_b, e_l_s, s_l_b, s_l_e))
return(res)
}
chrom <- 1
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 69 (96%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 3 (4.2%) | 0 (0%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 2 (1.0%) | 2 (1.5%) | 2 (2.8%) | 0 (0%) | 0 (0%) |
| TRUE | 199 (99%) | 135 (99%) | 70 (97%) | 107 (100%) | 85 (100%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 3 (2.2%) | 3 (4.2%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 134 (98%) | 69 (96%) | 107 (100%) | 85 (100%) |
| e_l_s | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 199 (99%) | 135 (99%) | 70 (97%) | 107 (100%) | 85 (100%) |
| TRUE | 2 (1.0%) | 2 (1.5%) | 2 (2.8%) | 0 (0%) | 0 (0%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 131 (96%) | 70 (97%) | 102 (95%) | 85 (100%) |
| TRUE | 0 (0%) | 6 (4.4%) | 2 (2.8%) | 5 (4.7%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 2 (1.0%) | 9 (6.6%) | 4 (5.6%) | 10 (9.3%) | 1 (1.2%) |
| TRUE | 199 (99%) | 128 (93%) | 68 (94%) | 97 (91%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 6 (4.4%) | 2 (2.8%) | 5 (4.7%) | 0 (0%) |
| TRUE | 201 (100%) | 131 (96%) | 70 (97%) | 102 (95%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 199 (99%) | 129 (94%) | 68 (94%) | 97 (91%) | 85 (100%) |
| TRUE | 2 (1.0%) | 8 (5.8%) | 4 (5.6%) | 10 (9.3%) | 0 (0%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 2
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 128 (93%) | 70 (97%) | 105 (98%) | 85 (100%) |
| TRUE | 0 (0%) | 9 (6.6%) | 2 (2.8%) | 2 (1.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 3 (1.5%) | 7 (5.1%) | 2 (2.8%) | 8 (7.5%) | 1 (1.2%) |
| TRUE | 198 (99%) | 130 (95%) | 70 (97%) | 99 (93%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 9 (6.6%) | 2 (2.8%) | 2 (1.9%) | 0 (0%) |
| TRUE | 201 (100%) | 128 (93%) | 70 (97%) | 105 (98%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 199 (99%) | 132 (96%) | 70 (97%) | 100 (93%) | 84 (99%) |
| TRUE | 2 (1.0%) | 5 (3.6%) | 2 (2.8%) | 7 (6.5%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 4 (2.0%) | 5 (3.6%) | 1 (1.4%) | 2 (1.9%) | 0 (0%) |
| TRUE | 197 (98%) | 132 (96%) | 71 (99%) | 105 (98%) | 85 (100%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 4 (2.9%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 201 (100%) | 133 (97%) | 72 (100%) | 106 (99%) | 85 (100%) |
| e_l_s | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 197 (98%) | 132 (96%) | 71 (99%) | 105 (98%) | 85 (100%) |
| TRUE | 4 (2.0%) | 5 (3.6%) | 1 (1.4%) | 2 (1.9%) | 0 (0%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 3
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 131 (96%) | 70 (97%) | 104 (97%) | 85 (100%) |
| TRUE | 0 (0%) | 6 (4.4%) | 2 (2.8%) | 3 (2.8%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 3 (1.5%) | 7 (5.1%) | 4 (5.6%) | 4 (3.7%) | 1 (1.2%) |
| TRUE | 198 (99%) | 130 (95%) | 68 (94%) | 103 (96%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 7 (5.1%) | 2 (2.8%) | 3 (2.8%) | 0 (0%) |
| TRUE | 201 (100%) | 130 (95%) | 70 (97%) | 104 (97%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 198 (99%) | 130 (95%) | 69 (96%) | 104 (97%) | 84 (99%) |
| TRUE | 3 (1.5%) | 7 (5.1%) | 3 (4.2%) | 3 (2.8%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 200 (100%) | 134 (98%) | 71 (99%) | 100 (93%) | 84 (99%) |
| TRUE | 1 (0.5%) | 3 (2.2%) | 1 (1.4%) | 7 (6.5%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 4 (2.0%) | 8 (5.8%) | 6 (8.3%) | 7 (6.5%) | 1 (1.2%) |
| TRUE | 197 (98%) | 129 (94%) | 66 (92%) | 100 (93%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 1 (0.5%) | 3 (2.2%) | 1 (1.4%) | 7 (6.5%) | 1 (1.2%) |
| TRUE | 200 (100%) | 134 (98%) | 71 (99%) | 100 (93%) | 84 (99%) |
| e_l_s | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 197 (98%) | 129 (94%) | 67 (93%) | 101 (94%) | 84 (99%) |
| TRUE | 4 (2.0%) | 8 (5.8%) | 5 (6.9%) | 6 (5.6%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 4
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 133 (97%) | 71 (99%) | 105 (98%) | 85 (100%) |
| TRUE | 0 (0%) | 4 (2.9%) | 1 (1.4%) | 2 (1.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 8 (4.0%) | 7 (5.1%) | 1 (1.4%) | 5 (4.7%) | 0 (0%) |
| TRUE | 193 (96%) | 130 (95%) | 71 (99%) | 102 (95%) | 85 (100%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 5 (3.6%) | 1 (1.4%) | 3 (2.8%) | 0 (0%) |
| TRUE | 201 (100%) | 132 (96%) | 71 (99%) | 104 (97%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 193 (96%) | 130 (95%) | 71 (99%) | 102 (95%) | 85 (100%) |
| TRUE | 8 (4.0%) | 7 (5.1%) | 1 (1.4%) | 5 (4.7%) | 0 (0%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 136 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 0 (0%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 130 (95%) | 68 (94%) | 105 (98%) | 85 (100%) |
| TRUE | 0 (0%) | 7 (5.1%) | 4 (5.6%) | 2 (1.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 10 (5.0%) | 16 (12%) | 4 (5.6%) | 6 (5.6%) | 3 (3.5%) |
| TRUE | 191 (95%) | 121 (88%) | 68 (94%) | 101 (94%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 7 (5.1%) | 5 (6.9%) | 2 (1.9%) | 0 (0%) |
| TRUE | 201 (100%) | 130 (95%) | 67 (93%) | 105 (98%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 6 (4.4%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 131 (96%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 192 (96%) | 122 (89%) | 69 (96%) | 101 (94%) | 83 (98%) |
| TRUE | 9 (4.5%) | 15 (11%) | 3 (4.2%) | 6 (5.6%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 131 (96%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 6 (4.4%) | 0 (0%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 5
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 127 (93%) | 70 (97%) | 105 (98%) | 83 (98%) |
| TRUE | 0 (0%) | 10 (7.3%) | 2 (2.8%) | 2 (1.9%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 2 (1.0%) | 7 (5.1%) | 6 (8.3%) | 5 (4.7%) | 1 (1.2%) |
| TRUE | 199 (99%) | 130 (95%) | 66 (92%) | 102 (95%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 10 (7.3%) | 3 (4.2%) | 2 (1.9%) | 2 (2.4%) |
| TRUE | 201 (100%) | 127 (93%) | 69 (96%) | 105 (98%) | 83 (98%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 1 (1.4%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 136 (99%) | 71 (99%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 199 (99%) | 131 (96%) | 66 (92%) | 102 (95%) | 84 (99%) |
| TRUE | 2 (1.0%) | 6 (4.4%) | 6 (8.3%) | 5 (4.7%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 136 (99%) | 71 (99%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 1 (1.4%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 129 (94%) | 69 (96%) | 105 (98%) | 85 (100%) |
| TRUE | 0 (0%) | 8 (5.8%) | 3 (4.2%) | 2 (1.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 10 (5.0%) | 9 (6.6%) | 2 (2.8%) | 6 (5.6%) | 1 (1.2%) |
| TRUE | 191 (95%) | 128 (93%) | 70 (97%) | 101 (94%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 8 (5.8%) | 3 (4.2%) | 2 (1.9%) | 0 (0%) |
| TRUE | 201 (100%) | 129 (94%) | 69 (96%) | 105 (98%) | 85 (100%) |
| e_l_s | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 191 (95%) | 129 (94%) | 70 (97%) | 101 (94%) | 84 (99%) |
| TRUE | 10 (5.0%) | 8 (5.8%) | 2 (2.8%) | 6 (5.6%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 6
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 118 (86%) | 66 (92%) | 98 (92%) | 83 (98%) |
| TRUE | 0 (0%) | 19 (14%) | 6 (8.3%) | 9 (8.4%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 3 (1.5%) | 9 (6.6%) | 2 (2.8%) | 7 (6.5%) | 1 (1.2%) |
| TRUE | 198 (99%) | 128 (93%) | 70 (97%) | 100 (93%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 19 (14%) | 6 (8.3%) | 9 (8.4%) | 2 (2.4%) |
| TRUE | 201 (100%) | 118 (86%) | 66 (92%) | 98 (92%) | 83 (98%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 7 (5.1%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 201 (100%) | 130 (95%) | 72 (100%) | 106 (99%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 199 (99%) | 128 (93%) | 70 (97%) | 102 (95%) | 84 (99%) |
| TRUE | 2 (1.0%) | 9 (6.6%) | 2 (2.8%) | 5 (4.7%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 131 (96%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 6 (4.4%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 127 (93%) | 70 (97%) | 105 (98%) | 85 (100%) |
| TRUE | 0 (0%) | 10 (7.3%) | 2 (2.8%) | 2 (1.9%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 6 (3.0%) | 12 (8.8%) | 3 (4.2%) | 8 (7.5%) | 2 (2.4%) |
| TRUE | 195 (97%) | 125 (91%) | 69 (96%) | 99 (93%) | 83 (98%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 10 (7.3%) | 2 (2.8%) | 4 (3.7%) | 0 (0%) |
| TRUE | 201 (100%) | 127 (93%) | 70 (97%) | 103 (96%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 3 (2.2%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 134 (98%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 195 (97%) | 127 (93%) | 69 (96%) | 100 (93%) | 83 (98%) |
| TRUE | 6 (3.0%) | 10 (7.3%) | 3 (4.2%) | 7 (6.5%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 0 (0%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 7
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 127 (93%) | 69 (96%) | 99 (93%) | 84 (99%) |
| TRUE | 0 (0%) | 10 (7.3%) | 3 (4.2%) | 8 (7.5%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 6 (3.0%) | 1 (0.7%) | 3 (4.2%) | 6 (5.6%) | 1 (1.2%) |
| TRUE | 195 (97%) | 136 (99%) | 69 (96%) | 101 (94%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 11 (8.0%) | 3 (4.2%) | 9 (8.4%) | 1 (1.2%) |
| TRUE | 201 (100%) | 126 (92%) | 69 (96%) | 98 (92%) | 84 (99%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 106 (99%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 195 (97%) | 136 (99%) | 69 (96%) | 101 (94%) | 84 (99%) |
| TRUE | 6 (3.0%) | 1 (0.7%) | 3 (4.2%) | 6 (5.6%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 0 (0%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 200 (100%) | 133 (97%) | 71 (99%) | 105 (98%) | 83 (98%) |
| TRUE | 1 (0.5%) | 4 (2.9%) | 1 (1.4%) | 2 (1.9%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 8 (4.0%) | 13 (9.5%) | 5 (6.9%) | 6 (5.6%) | 2 (2.4%) |
| TRUE | 193 (96%) | 124 (91%) | 67 (93%) | 101 (94%) | 83 (98%) |
| e_l_b | |||||
| FALSE | 1 (0.5%) | 4 (2.9%) | 1 (1.4%) | 2 (1.9%) | 2 (2.4%) |
| TRUE | 200 (100%) | 133 (97%) | 71 (99%) | 105 (98%) | 83 (98%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 3 (2.2%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 134 (98%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 195 (97%) | 124 (91%) | 67 (93%) | 101 (94%) | 83 (98%) |
| TRUE | 6 (3.0%) | 13 (9.5%) | 5 (6.9%) | 6 (5.6%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 0 (0%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 8
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 63 (31%) | 35 (26%) | 1 (1.4%) | 20 (19%) | 29 (34%) |
| TRUE | 138 (69%) | 102 (74%) | 71 (99%) | 87 (81%) | 56 (66%) |
| b_l_s | |||||
| FALSE | 81 (40%) | 44 (32%) | 49 (68%) | 41 (38%) | 32 (38%) |
| TRUE | 120 (60%) | 93 (68%) | 23 (32%) | 66 (62%) | 53 (62%) |
| e_l_b | |||||
| FALSE | 138 (69%) | 102 (74%) | 71 (99%) | 87 (81%) | 57 (67%) |
| TRUE | 63 (31%) | 35 (26%) | 1 (1.4%) | 20 (19%) | 28 (33%) |
| e_l_s | |||||
| FALSE | 140 (70%) | 100 (73%) | 69 (96%) | 87 (81%) | 56 (66%) |
| TRUE | 61 (30%) | 37 (27%) | 3 (4.2%) | 20 (19%) | 29 (34%) |
| s_l_b | |||||
| FALSE | 124 (62%) | 96 (70%) | 29 (40%) | 68 (64%) | 55 (65%) |
| TRUE | 77 (38%) | 41 (30%) | 43 (60%) | 39 (36%) | 30 (35%) |
| s_l_e | |||||
| FALSE | 61 (30%) | 37 (27%) | 3 (4.2%) | 20 (19%) | 29 (34%) |
| TRUE | 140 (70%) | 100 (73%) | 69 (96%) | 87 (81%) | 56 (66%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 126 (92%) | 70 (97%) | 100 (93%) | 84 (99%) |
| TRUE | 0 (0%) | 11 (8.0%) | 2 (2.8%) | 7 (6.5%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 5 (2.5%) | 11 (8.0%) | 13 (18%) | 14 (13%) | 4 (4.7%) |
| TRUE | 196 (98%) | 126 (92%) | 59 (82%) | 93 (87%) | 81 (95%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 11 (8.0%) | 2 (2.8%) | 7 (6.5%) | 1 (1.2%) |
| TRUE | 201 (100%) | 126 (92%) | 70 (97%) | 100 (93%) | 84 (99%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 5 (3.6%) | 2 (2.8%) | 2 (1.9%) | 1 (1.2%) |
| TRUE | 201 (100%) | 132 (96%) | 70 (97%) | 105 (98%) | 84 (99%) |
| s_l_b | |||||
| FALSE | 196 (98%) | 126 (92%) | 59 (82%) | 93 (87%) | 81 (95%) |
| TRUE | 5 (2.5%) | 11 (8.0%) | 13 (18%) | 14 (13%) | 4 (4.7%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 132 (96%) | 70 (97%) | 105 (98%) | 84 (99%) |
| TRUE | 0 (0%) | 5 (3.6%) | 2 (2.8%) | 2 (1.9%) | 1 (1.2%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 9
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 125 (91%) | 68 (94%) | 98 (92%) | 84 (99%) |
| TRUE | 0 (0%) | 12 (8.8%) | 4 (5.6%) | 9 (8.4%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 11 (5.5%) | 7 (5.1%) | 4 (5.6%) | 10 (9.3%) | 4 (4.7%) |
| TRUE | 190 (95%) | 130 (95%) | 68 (94%) | 97 (91%) | 81 (95%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 14 (10%) | 4 (5.6%) | 10 (9.3%) | 1 (1.2%) |
| TRUE | 201 (100%) | 123 (90%) | 68 (94%) | 97 (91%) | 84 (99%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 4 (2.9%) | 1 (1.4%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 133 (97%) | 71 (99%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 191 (95%) | 130 (95%) | 68 (94%) | 97 (91%) | 82 (96%) |
| TRUE | 10 (5.0%) | 7 (5.1%) | 4 (5.6%) | 10 (9.3%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 133 (97%) | 71 (99%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 4 (2.9%) | 1 (1.4%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 128 (93%) | 71 (99%) | 100 (93%) | 85 (100%) |
| TRUE | 0 (0%) | 9 (6.6%) | 1 (1.4%) | 7 (6.5%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 8 (4.0%) | 8 (5.8%) | 4 (5.6%) | 14 (13%) | 3 (3.5%) |
| TRUE | 193 (96%) | 129 (94%) | 68 (94%) | 93 (87%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 9 (6.6%) | 1 (1.4%) | 8 (7.5%) | 0 (0%) |
| TRUE | 201 (100%) | 128 (93%) | 71 (99%) | 99 (93%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 4 (2.9%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 133 (97%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 193 (96%) | 129 (94%) | 68 (94%) | 96 (90%) | 82 (96%) |
| TRUE | 8 (4.0%) | 8 (5.8%) | 4 (5.6%) | 11 (10%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 133 (97%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 4 (2.9%) | 0 (0%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 10
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 131 (96%) | 63 (88%) | 102 (95%) | 81 (95%) |
| TRUE | 0 (0%) | 6 (4.4%) | 9 (13%) | 5 (4.7%) | 4 (4.7%) |
| b_l_s | |||||
| FALSE | 5 (2.5%) | 6 (4.4%) | 5 (6.9%) | 11 (10%) | 1 (1.2%) |
| TRUE | 196 (98%) | 131 (96%) | 67 (93%) | 96 (90%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 6 (4.4%) | 9 (13%) | 7 (6.5%) | 4 (4.7%) |
| TRUE | 201 (100%) | 131 (96%) | 63 (88%) | 100 (93%) | 81 (95%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 2 (2.8%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 136 (99%) | 70 (97%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 197 (98%) | 131 (96%) | 67 (93%) | 97 (91%) | 84 (99%) |
| TRUE | 4 (2.0%) | 6 (4.4%) | 5 (6.9%) | 10 (9.3%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 136 (99%) | 70 (97%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 2 (2.8%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 130 (95%) | 68 (94%) | 103 (96%) | 84 (99%) |
| TRUE | 0 (0%) | 7 (5.1%) | 4 (5.6%) | 4 (3.7%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 6 (3.0%) | 18 (13%) | 4 (5.6%) | 12 (11%) | 2 (2.4%) |
| TRUE | 195 (97%) | 119 (87%) | 68 (94%) | 95 (89%) | 83 (98%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 8 (5.8%) | 5 (6.9%) | 4 (3.7%) | 2 (2.4%) |
| TRUE | 201 (100%) | 129 (94%) | 67 (93%) | 103 (96%) | 83 (98%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 1 (0.7%) | 1 (1.4%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 136 (99%) | 71 (99%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 196 (98%) | 120 (88%) | 68 (94%) | 96 (90%) | 83 (98%) |
| TRUE | 5 (2.5%) | 17 (12%) | 4 (5.6%) | 11 (10%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 136 (99%) | 71 (99%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 1 (1.4%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 11
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 124 (91%) | 68 (94%) | 101 (94%) | 84 (99%) |
| TRUE | 0 (0%) | 13 (9.5%) | 4 (5.6%) | 6 (5.6%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 8 (4.0%) | 13 (9.5%) | 8 (11%) | 16 (15%) | 2 (2.4%) |
| TRUE | 193 (96%) | 124 (91%) | 64 (89%) | 91 (85%) | 83 (98%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 14 (10%) | 5 (6.9%) | 6 (5.6%) | 1 (1.2%) |
| TRUE | 201 (100%) | 123 (90%) | 67 (93%) | 101 (94%) | 84 (99%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 6 (4.4%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 201 (100%) | 131 (96%) | 72 (100%) | 106 (99%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 195 (97%) | 125 (91%) | 66 (92%) | 91 (85%) | 83 (98%) |
| TRUE | 6 (3.0%) | 12 (8.8%) | 6 (8.3%) | 16 (15%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 132 (96%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 5 (3.6%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 125 (91%) | 71 (99%) | 101 (94%) | 85 (100%) |
| TRUE | 0 (0%) | 12 (8.8%) | 1 (1.4%) | 6 (5.6%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 4 (2.0%) | 13 (9.5%) | 4 (5.6%) | 9 (8.4%) | 2 (2.4%) |
| TRUE | 197 (98%) | 124 (91%) | 68 (94%) | 98 (92%) | 83 (98%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 12 (8.8%) | 1 (1.4%) | 6 (5.6%) | 0 (0%) |
| TRUE | 201 (100%) | 125 (91%) | 71 (99%) | 101 (94%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 5 (3.6%) | 1 (1.4%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 132 (96%) | 71 (99%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 197 (98%) | 124 (91%) | 68 (94%) | 99 (93%) | 84 (99%) |
| TRUE | 4 (2.0%) | 13 (9.5%) | 4 (5.6%) | 8 (7.5%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 133 (97%) | 71 (99%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 4 (2.9%) | 1 (1.4%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 12
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 126 (92%) | 67 (93%) | 103 (96%) | 83 (98%) |
| TRUE | 0 (0%) | 11 (8.0%) | 5 (6.9%) | 4 (3.7%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 13 (6.5%) | 13 (9.5%) | 6 (8.3%) | 7 (6.5%) | 4 (4.7%) |
| TRUE | 188 (94%) | 124 (91%) | 66 (92%) | 100 (93%) | 81 (95%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 12 (8.8%) | 5 (6.9%) | 4 (3.7%) | 2 (2.4%) |
| TRUE | 201 (100%) | 125 (91%) | 67 (93%) | 103 (96%) | 83 (98%) |
| e_l_s | |||||
| TRUE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 188 (94%) | 125 (91%) | 68 (94%) | 101 (94%) | 82 (96%) |
| TRUE | 13 (6.5%) | 12 (8.8%) | 4 (5.6%) | 6 (5.6%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 137 (100%) | 72 (100%) | 107 (100%) | 85 (100%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 131 (96%) | 69 (96%) | 104 (97%) | 83 (98%) |
| TRUE | 0 (0%) | 6 (4.4%) | 3 (4.2%) | 3 (2.8%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 3 (1.5%) | 13 (9.5%) | 8 (11%) | 9 (8.4%) | 1 (1.2%) |
| TRUE | 198 (99%) | 124 (91%) | 64 (89%) | 98 (92%) | 84 (99%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 6 (4.4%) | 3 (4.2%) | 3 (2.8%) | 2 (2.4%) |
| TRUE | 201 (100%) | 131 (96%) | 69 (96%) | 104 (97%) | 83 (98%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 198 (99%) | 125 (91%) | 64 (89%) | 99 (93%) | 84 (99%) |
| TRUE | 3 (1.5%) | 12 (8.8%) | 8 (11%) | 8 (7.5%) | 1 (1.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 135 (99%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 2 (1.5%) | 0 (0%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 13
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 200 (100%) | 121 (88%) | 69 (96%) | 101 (94%) | 84 (99%) |
| TRUE | 1 (0.5%) | 16 (12%) | 3 (4.2%) | 6 (5.6%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 14 (7.0%) | 11 (8.0%) | 9 (13%) | 11 (10%) | 4 (4.7%) |
| TRUE | 187 (93%) | 126 (92%) | 63 (88%) | 96 (90%) | 81 (95%) |
| e_l_b | |||||
| FALSE | 1 (0.5%) | 18 (13%) | 4 (5.6%) | 6 (5.6%) | 1 (1.2%) |
| TRUE | 200 (100%) | 119 (87%) | 68 (94%) | 101 (94%) | 84 (99%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 4 (2.9%) | 2 (2.8%) | 0 (0%) | 1 (1.2%) |
| TRUE | 201 (100%) | 133 (97%) | 70 (97%) | 107 (100%) | 84 (99%) |
| s_l_b | |||||
| FALSE | 187 (93%) | 127 (93%) | 63 (88%) | 98 (92%) | 83 (98%) |
| TRUE | 14 (7.0%) | 10 (7.3%) | 9 (13%) | 9 (8.4%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 133 (97%) | 70 (97%) | 107 (100%) | 84 (99%) |
| TRUE | 0 (0%) | 4 (2.9%) | 2 (2.8%) | 0 (0%) | 1 (1.2%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 200 (100%) | 129 (94%) | 68 (94%) | 96 (90%) | 76 (89%) |
| TRUE | 1 (0.5%) | 8 (5.8%) | 4 (5.6%) | 11 (10%) | 9 (11%) |
| b_l_s | |||||
| FALSE | 11 (5.5%) | 11 (8.0%) | 9 (13%) | 18 (17%) | 5 (5.9%) |
| TRUE | 190 (95%) | 126 (92%) | 63 (88%) | 89 (83%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 1 (0.5%) | 9 (6.6%) | 4 (5.6%) | 11 (10%) | 9 (11%) |
| TRUE | 200 (100%) | 128 (93%) | 68 (94%) | 96 (90%) | 76 (89%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 4 (2.9%) | 1 (1.4%) | 1 (0.9%) | 1 (1.2%) |
| TRUE | 201 (100%) | 133 (97%) | 71 (99%) | 106 (99%) | 84 (99%) |
| s_l_b | |||||
| FALSE | 190 (95%) | 127 (93%) | 64 (89%) | 90 (84%) | 80 (94%) |
| TRUE | 11 (5.5%) | 10 (7.3%) | 8 (11%) | 17 (16%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 72 (100%) | 106 (99%) | 84 (99%) |
| TRUE | 0 (0%) | 3 (2.2%) | 0 (0%) | 1 (0.9%) | 1 (1.2%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 14
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 200 (100%) | 115 (84%) | 59 (82%) | 90 (84%) | 82 (96%) |
| TRUE | 1 (0.5%) | 22 (16%) | 13 (18%) | 17 (16%) | 3 (3.5%) |
| b_l_s | |||||
| FALSE | 9 (4.5%) | 16 (12%) | 8 (11%) | 16 (15%) | 6 (7.1%) |
| TRUE | 192 (96%) | 121 (88%) | 64 (89%) | 91 (85%) | 79 (93%) |
| e_l_b | |||||
| FALSE | 1 (0.5%) | 22 (16%) | 13 (18%) | 18 (17%) | 4 (4.7%) |
| TRUE | 200 (100%) | 115 (84%) | 59 (82%) | 89 (83%) | 81 (95%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 3 (2.2%) | 1 (1.4%) | 4 (3.7%) | 0 (0%) |
| TRUE | 201 (100%) | 134 (98%) | 71 (99%) | 103 (96%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 193 (96%) | 122 (89%) | 64 (89%) | 91 (85%) | 79 (93%) |
| TRUE | 8 (4.0%) | 15 (11%) | 8 (11%) | 16 (15%) | 6 (7.1%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 71 (99%) | 103 (96%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 1 (1.4%) | 4 (3.7%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 122 (89%) | 64 (89%) | 98 (92%) | 83 (98%) |
| TRUE | 0 (0%) | 15 (11%) | 8 (11%) | 9 (8.4%) | 2 (2.4%) |
| b_l_s | |||||
| FALSE | 7 (3.5%) | 12 (8.8%) | 9 (13%) | 13 (12%) | 5 (5.9%) |
| TRUE | 194 (97%) | 125 (91%) | 63 (88%) | 94 (88%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 16 (12%) | 8 (11%) | 12 (11%) | 2 (2.4%) |
| TRUE | 201 (100%) | 121 (88%) | 64 (89%) | 95 (89%) | 83 (98%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 2 (1.5%) | 1 (1.4%) | 1 (0.9%) | 0 (0%) |
| TRUE | 201 (100%) | 135 (99%) | 71 (99%) | 106 (99%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 194 (97%) | 125 (91%) | 63 (88%) | 96 (90%) | 80 (94%) |
| TRUE | 7 (3.5%) | 12 (8.8%) | 9 (13%) | 11 (10%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 135 (99%) | 71 (99%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 2 (1.5%) | 1 (1.4%) | 1 (0.9%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 15
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 194 (97%) | 122 (89%) | 65 (90%) | 90 (84%) | 81 (95%) |
| TRUE | 7 (3.5%) | 15 (11%) | 7 (9.7%) | 17 (16%) | 4 (4.7%) |
| b_l_s | |||||
| FALSE | 11 (5.5%) | 14 (10%) | 8 (11%) | 19 (18%) | 3 (3.5%) |
| TRUE | 190 (95%) | 123 (90%) | 64 (89%) | 88 (82%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 7 (3.5%) | 17 (12%) | 8 (11%) | 18 (17%) | 5 (5.9%) |
| TRUE | 194 (97%) | 120 (88%) | 64 (89%) | 89 (83%) | 80 (94%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 5 (3.6%) | 0 (0%) | 3 (2.8%) | 0 (0%) |
| TRUE | 201 (100%) | 132 (96%) | 72 (100%) | 104 (97%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 192 (96%) | 124 (91%) | 67 (93%) | 90 (84%) | 83 (98%) |
| TRUE | 9 (4.5%) | 13 (9.5%) | 5 (6.9%) | 17 (16%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 133 (97%) | 72 (100%) | 105 (98%) | 85 (100%) |
| TRUE | 0 (0%) | 4 (2.9%) | 0 (0%) | 2 (1.9%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 196 (98%) | 129 (94%) | 66 (92%) | 100 (93%) | 80 (94%) |
| TRUE | 5 (2.5%) | 8 (5.8%) | 6 (8.3%) | 7 (6.5%) | 5 (5.9%) |
| b_l_s | |||||
| FALSE | 12 (6.0%) | 15 (11%) | 8 (11%) | 21 (20%) | 0 (0%) |
| TRUE | 189 (94%) | 122 (89%) | 64 (89%) | 86 (80%) | 85 (100%) |
| e_l_b | |||||
| FALSE | 5 (2.5%) | 12 (8.8%) | 7 (9.7%) | 8 (7.5%) | 5 (5.9%) |
| TRUE | 196 (98%) | 125 (91%) | 65 (90%) | 99 (93%) | 80 (94%) |
| e_l_s | |||||
| FALSE | 2 (1.0%) | 4 (2.9%) | 0 (0%) | 3 (2.8%) | 0 (0%) |
| TRUE | 199 (99%) | 133 (97%) | 72 (100%) | 104 (97%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 191 (95%) | 125 (91%) | 64 (89%) | 87 (81%) | 85 (100%) |
| TRUE | 10 (5.0%) | 12 (8.8%) | 8 (11%) | 20 (19%) | 0 (0%) |
| s_l_e | |||||
| FALSE | 200 (100%) | 133 (97%) | 72 (100%) | 104 (97%) | 85 (100%) |
| TRUE | 1 (0.5%) | 4 (2.9%) | 0 (0%) | 3 (2.8%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 16
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 128 (93%) | 68 (94%) | 100 (93%) | 85 (100%) |
| TRUE | 0 (0%) | 9 (6.6%) | 4 (5.6%) | 7 (6.5%) | 0 (0%) |
| b_l_s | |||||
| FALSE | 6 (3.0%) | 13 (9.5%) | 7 (9.7%) | 8 (7.5%) | 4 (4.7%) |
| TRUE | 195 (97%) | 124 (91%) | 65 (90%) | 99 (93%) | 81 (95%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 10 (7.3%) | 5 (6.9%) | 7 (6.5%) | 0 (0%) |
| TRUE | 201 (100%) | 127 (93%) | 67 (93%) | 100 (93%) | 85 (100%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 2 (1.5%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| TRUE | 201 (100%) | 135 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 195 (97%) | 124 (91%) | 66 (92%) | 99 (93%) | 81 (95%) |
| TRUE | 6 (3.0%) | 13 (9.5%) | 6 (8.3%) | 8 (7.5%) | 4 (4.7%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 135 (99%) | 72 (100%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 2 (1.5%) | 0 (0%) | 1 (0.9%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 128 (93%) | 70 (97%) | 92 (86%) | 82 (96%) |
| TRUE | 0 (0%) | 9 (6.6%) | 2 (2.8%) | 15 (14%) | 3 (3.5%) |
| b_l_s | |||||
| FALSE | 10 (5.0%) | 13 (9.5%) | 15 (21%) | 12 (11%) | 9 (11%) |
| TRUE | 191 (95%) | 124 (91%) | 57 (79%) | 95 (89%) | 76 (89%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 9 (6.6%) | 2 (2.8%) | 16 (15%) | 3 (3.5%) |
| TRUE | 201 (100%) | 128 (93%) | 70 (97%) | 91 (85%) | 82 (96%) |
| e_l_s | |||||
| FALSE | 3 (1.5%) | 1 (0.7%) | 1 (1.4%) | 1 (0.9%) | 2 (2.4%) |
| TRUE | 198 (99%) | 136 (99%) | 71 (99%) | 106 (99%) | 83 (98%) |
| s_l_b | |||||
| FALSE | 192 (96%) | 126 (92%) | 59 (82%) | 96 (90%) | 76 (89%) |
| TRUE | 9 (4.5%) | 11 (8.0%) | 13 (18%) | 11 (10%) | 9 (11%) |
| s_l_e | |||||
| FALSE | 198 (99%) | 137 (100%) | 71 (99%) | 106 (99%) | 83 (98%) |
| TRUE | 3 (1.5%) | 0 (0%) | 1 (1.4%) | 1 (0.9%) | 2 (2.4%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 17
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 200 (100%) | 125 (91%) | 66 (92%) | 89 (83%) | 79 (93%) |
| TRUE | 1 (0.5%) | 12 (8.8%) | 6 (8.3%) | 18 (17%) | 6 (7.1%) |
| b_l_s | |||||
| FALSE | 10 (5.0%) | 15 (11%) | 9 (13%) | 18 (17%) | 5 (5.9%) |
| TRUE | 191 (95%) | 122 (89%) | 63 (88%) | 89 (83%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 2 (1.0%) | 14 (10%) | 6 (8.3%) | 21 (20%) | 6 (7.1%) |
| TRUE | 199 (99%) | 123 (90%) | 66 (92%) | 86 (80%) | 79 (93%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 3 (2.2%) | 0 (0%) | 0 (0%) | 0 (0%) |
| TRUE | 201 (100%) | 134 (98%) | 72 (100%) | 107 (100%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 192 (96%) | 122 (89%) | 63 (88%) | 90 (84%) | 81 (95%) |
| TRUE | 9 (4.5%) | 15 (11%) | 9 (13%) | 17 (16%) | 4 (4.7%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 72 (100%) | 107 (100%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 0 (0%) | 0 (0%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 183 (91%) | 128 (93%) | 67 (93%) | 99 (93%) | 82 (96%) |
| TRUE | 18 (9.0%) | 9 (6.6%) | 5 (6.9%) | 8 (7.5%) | 3 (3.5%) |
| b_l_s | |||||
| FALSE | 14 (7.0%) | 12 (8.8%) | 13 (18%) | 20 (19%) | 5 (5.9%) |
| TRUE | 187 (93%) | 125 (91%) | 59 (82%) | 87 (81%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 18 (9.0%) | 9 (6.6%) | 5 (6.9%) | 8 (7.5%) | 3 (3.5%) |
| TRUE | 183 (91%) | 128 (93%) | 67 (93%) | 99 (93%) | 82 (96%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 2 (1.5%) | 1 (1.4%) | 1 (0.9%) | 0 (0%) |
| TRUE | 201 (100%) | 135 (99%) | 71 (99%) | 106 (99%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 189 (94%) | 125 (91%) | 59 (82%) | 91 (85%) | 80 (94%) |
| TRUE | 12 (6.0%) | 12 (8.8%) | 13 (18%) | 16 (15%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 136 (99%) | 71 (99%) | 106 (99%) | 85 (100%) |
| TRUE | 0 (0%) | 1 (0.7%) | 1 (1.4%) | 1 (0.9%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 18
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 200 (100%) | 120 (88%) | 64 (89%) | 93 (87%) | 78 (92%) |
| TRUE | 1 (0.5%) | 17 (12%) | 8 (11%) | 14 (13%) | 7 (8.2%) |
| b_l_s | |||||
| FALSE | 16 (8.0%) | 17 (12%) | 9 (13%) | 22 (21%) | 3 (3.5%) |
| TRUE | 185 (92%) | 120 (88%) | 63 (88%) | 85 (79%) | 82 (96%) |
| e_l_b | |||||
| FALSE | 1 (0.5%) | 17 (12%) | 8 (11%) | 14 (13%) | 7 (8.2%) |
| TRUE | 200 (100%) | 120 (88%) | 64 (89%) | 93 (87%) | 78 (92%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 3 (2.2%) | 3 (4.2%) | 3 (2.8%) | 0 (0%) |
| TRUE | 201 (100%) | 134 (98%) | 69 (96%) | 104 (97%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 185 (92%) | 120 (88%) | 63 (88%) | 87 (81%) | 83 (98%) |
| TRUE | 16 (8.0%) | 17 (12%) | 9 (13%) | 20 (19%) | 2 (2.4%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 69 (96%) | 104 (97%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 3 (4.2%) | 3 (2.8%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 199 (99%) | 126 (92%) | 68 (94%) | 95 (89%) | 81 (95%) |
| TRUE | 2 (1.0%) | 11 (8.0%) | 4 (5.6%) | 12 (11%) | 4 (4.7%) |
| b_l_s | |||||
| FALSE | 6 (3.0%) | 14 (10%) | 11 (15%) | 19 (18%) | 9 (11%) |
| TRUE | 195 (97%) | 123 (90%) | 61 (85%) | 88 (82%) | 76 (89%) |
| e_l_b | |||||
| FALSE | 2 (1.0%) | 12 (8.8%) | 5 (6.9%) | 14 (13%) | 4 (4.7%) |
| TRUE | 199 (99%) | 125 (91%) | 67 (93%) | 93 (87%) | 81 (95%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 0 (0%) | 1 (1.4%) | 1 (0.9%) | 1 (1.2%) |
| TRUE | 201 (100%) | 137 (100%) | 71 (99%) | 106 (99%) | 84 (99%) |
| s_l_b | |||||
| FALSE | 195 (97%) | 125 (91%) | 62 (86%) | 88 (82%) | 76 (89%) |
| TRUE | 6 (3.0%) | 12 (8.8%) | 10 (14%) | 19 (18%) | 9 (11%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 137 (100%) | 71 (99%) | 106 (99%) | 84 (99%) |
| TRUE | 0 (0%) | 0 (0%) | 1 (1.4%) | 1 (0.9%) | 1 (1.2%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 19
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 199 (99%) | 113 (82%) | 61 (85%) | 93 (87%) | 82 (96%) |
| TRUE | 2 (1.0%) | 24 (18%) | 11 (15%) | 14 (13%) | 3 (3.5%) |
| b_l_s | |||||
| FALSE | 20 (10.0%) | 12 (8.8%) | 12 (17%) | 23 (21%) | 5 (5.9%) |
| TRUE | 181 (90%) | 125 (91%) | 60 (83%) | 84 (79%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 2 (1.0%) | 25 (18%) | 11 (15%) | 16 (15%) | 4 (4.7%) |
| TRUE | 199 (99%) | 112 (82%) | 61 (85%) | 91 (85%) | 81 (95%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 4 (2.9%) | 3 (4.2%) | 5 (4.7%) | 0 (0%) |
| TRUE | 201 (100%) | 133 (97%) | 69 (96%) | 102 (95%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 182 (91%) | 127 (93%) | 62 (86%) | 86 (80%) | 80 (94%) |
| TRUE | 19 (9.5%) | 10 (7.3%) | 10 (14%) | 21 (20%) | 5 (5.9%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 133 (97%) | 69 (96%) | 103 (96%) | 85 (100%) |
| TRUE | 0 (0%) | 4 (2.9%) | 3 (4.2%) | 4 (3.7%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 198 (99%) | 127 (93%) | 64 (89%) | 93 (87%) | 81 (95%) |
| TRUE | 3 (1.5%) | 10 (7.3%) | 8 (11%) | 14 (13%) | 4 (4.7%) |
| b_l_s | |||||
| FALSE | 22 (11%) | 17 (12%) | 15 (21%) | 24 (22%) | 5 (5.9%) |
| TRUE | 179 (89%) | 120 (88%) | 57 (79%) | 83 (78%) | 80 (94%) |
| e_l_b | |||||
| FALSE | 3 (1.5%) | 12 (8.8%) | 9 (13%) | 14 (13%) | 4 (4.7%) |
| TRUE | 198 (99%) | 125 (91%) | 63 (88%) | 93 (87%) | 81 (95%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 4 (2.9%) | 2 (2.8%) | 4 (3.7%) | 0 (0%) |
| TRUE | 201 (100%) | 133 (97%) | 70 (97%) | 103 (96%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 180 (90%) | 123 (90%) | 58 (81%) | 85 (79%) | 82 (96%) |
| TRUE | 21 (10%) | 14 (10%) | 14 (19%) | 22 (21%) | 3 (3.5%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 133 (97%) | 70 (97%) | 104 (97%) | 85 (100%) |
| TRUE | 0 (0%) | 4 (2.9%) | 2 (2.8%) | 3 (2.8%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 20
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 201 (100%) | 126 (92%) | 62 (86%) | 91 (85%) | 81 (95%) |
| TRUE | 0 (0%) | 11 (8.0%) | 10 (14%) | 16 (15%) | 4 (4.7%) |
| b_l_s | |||||
| FALSE | 28 (14%) | 23 (17%) | 8 (11%) | 10 (9.3%) | 12 (14%) |
| TRUE | 173 (86%) | 114 (83%) | 64 (89%) | 97 (91%) | 73 (86%) |
| e_l_b | |||||
| FALSE | 0 (0%) | 11 (8.0%) | 12 (17%) | 17 (16%) | 4 (4.7%) |
| TRUE | 201 (100%) | 126 (92%) | 60 (83%) | 90 (84%) | 81 (95%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 6 (4.4%) | 1 (1.4%) | 2 (1.9%) | 0 (0%) |
| TRUE | 201 (100%) | 131 (96%) | 71 (99%) | 105 (98%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 175 (87%) | 114 (83%) | 64 (89%) | 98 (92%) | 74 (87%) |
| TRUE | 26 (13%) | 23 (17%) | 8 (11%) | 9 (8.4%) | 11 (13%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 131 (96%) | 71 (99%) | 105 (98%) | 85 (100%) |
| TRUE | 0 (0%) | 6 (4.4%) | 1 (1.4%) | 2 (1.9%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 198 (99%) | 121 (88%) | 62 (86%) | 89 (83%) | 84 (99%) |
| TRUE | 3 (1.5%) | 16 (12%) | 10 (14%) | 18 (17%) | 1 (1.2%) |
| b_l_s | |||||
| FALSE | 24 (12%) | 21 (15%) | 8 (11%) | 20 (19%) | 7 (8.2%) |
| TRUE | 177 (88%) | 116 (85%) | 64 (89%) | 87 (81%) | 78 (92%) |
| e_l_b | |||||
| FALSE | 3 (1.5%) | 16 (12%) | 10 (14%) | 19 (18%) | 2 (2.4%) |
| TRUE | 198 (99%) | 121 (88%) | 62 (86%) | 88 (82%) | 83 (98%) |
| e_l_s | |||||
| FALSE | 0 (0%) | 4 (2.9%) | 2 (2.8%) | 4 (3.7%) | 0 (0%) |
| TRUE | 201 (100%) | 133 (97%) | 70 (97%) | 103 (96%) | 85 (100%) |
| s_l_b | |||||
| FALSE | 179 (89%) | 117 (85%) | 64 (89%) | 88 (82%) | 78 (92%) |
| TRUE | 22 (11%) | 20 (15%) | 8 (11%) | 19 (18%) | 7 (8.2%) |
| s_l_e | |||||
| FALSE | 201 (100%) | 134 (98%) | 70 (97%) | 103 (96%) | 85 (100%) |
| TRUE | 0 (0%) | 3 (2.2%) | 2 (2.8%) | 4 (3.7%) | 0 (0%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 21
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 187 (93%) | 97 (71%) | 56 (78%) | 76 (71%) | 69 (81%) |
| TRUE | 14 (7.0%) | 40 (29%) | 16 (22%) | 31 (29%) | 16 (19%) |
| b_l_s | |||||
| FALSE | 26 (13%) | 19 (14%) | 17 (24%) | 19 (18%) | 8 (9.4%) |
| TRUE | 175 (87%) | 118 (86%) | 55 (76%) | 88 (82%) | 77 (91%) |
| e_l_b | |||||
| FALSE | 15 (7.5%) | 43 (31%) | 19 (26%) | 32 (30%) | 17 (20%) |
| TRUE | 186 (93%) | 94 (69%) | 53 (74%) | 75 (70%) | 68 (80%) |
| e_l_s | |||||
| FALSE | 4 (2.0%) | 13 (9.5%) | 9 (13%) | 13 (12%) | 1 (1.2%) |
| TRUE | 197 (98%) | 124 (91%) | 63 (88%) | 94 (88%) | 84 (99%) |
| s_l_b | |||||
| FALSE | 177 (88%) | 122 (89%) | 55 (76%) | 92 (86%) | 77 (91%) |
| TRUE | 24 (12%) | 15 (11%) | 17 (24%) | 15 (14%) | 8 (9.4%) |
| s_l_e | |||||
| FALSE | 198 (99%) | 125 (91%) | 65 (90%) | 95 (89%) | 85 (100%) |
| TRUE | 3 (1.5%) | 12 (8.8%) | 7 (9.7%) | 12 (11%) | 0 (0%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 193 (96%) | 105 (77%) | 60 (83%) | 84 (79%) | 73 (86%) |
| TRUE | 8 (4.0%) | 32 (23%) | 12 (17%) | 23 (21%) | 12 (14%) |
| b_l_s | |||||
| FALSE | 29 (14%) | 24 (18%) | 17 (24%) | 20 (19%) | 13 (15%) |
| TRUE | 172 (86%) | 113 (82%) | 55 (76%) | 87 (81%) | 72 (85%) |
| e_l_b | |||||
| FALSE | 10 (5.0%) | 37 (27%) | 12 (17%) | 26 (24%) | 13 (15%) |
| TRUE | 191 (95%) | 100 (73%) | 60 (83%) | 81 (76%) | 72 (85%) |
| e_l_s | |||||
| FALSE | 1 (0.5%) | 16 (12%) | 3 (4.2%) | 5 (4.7%) | 3 (3.5%) |
| TRUE | 200 (100%) | 121 (88%) | 69 (96%) | 102 (95%) | 82 (96%) |
| s_l_b | |||||
| FALSE | 178 (89%) | 113 (82%) | 57 (79%) | 87 (81%) | 73 (86%) |
| TRUE | 23 (11%) | 24 (18%) | 15 (21%) | 20 (19%) | 12 (14%) |
| s_l_e | |||||
| FALSE | 200 (100%) | 122 (89%) | 69 (96%) | 102 (95%) | 82 (96%) |
| TRUE | 1 (0.5%) | 15 (11%) | 3 (4.2%) | 5 (4.7%) | 3 (3.5%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

chrom <- 22
plot_flips(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "Eagle", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flips(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flips_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SHAPEIT", "Eagle", "SUPER", chrom)

table_flip(df_switch_trio[[chrom]], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 184 (92%) | 109 (80%) | 48 (67%) | 76 (71%) | 65 (76%) |
| TRUE | 17 (8.5%) | 28 (20%) | 24 (33%) | 31 (29%) | 20 (24%) |
| b_l_s | |||||
| FALSE | 27 (13%) | 21 (15%) | 15 (21%) | 18 (17%) | 17 (20%) |
| TRUE | 174 (87%) | 116 (85%) | 57 (79%) | 89 (83%) | 68 (80%) |
| e_l_b | |||||
| FALSE | 18 (9.0%) | 34 (25%) | 25 (35%) | 37 (35%) | 22 (26%) |
| TRUE | 183 (91%) | 103 (75%) | 47 (65%) | 70 (65%) | 63 (74%) |
| e_l_s | |||||
| FALSE | 2 (1.0%) | 18 (13%) | 5 (6.9%) | 12 (11%) | 3 (3.5%) |
| TRUE | 199 (99%) | 119 (87%) | 67 (93%) | 95 (89%) | 82 (96%) |
| s_l_b | |||||
| FALSE | 178 (89%) | 117 (85%) | 59 (82%) | 91 (85%) | 68 (80%) |
| TRUE | 23 (11%) | 20 (15%) | 13 (18%) | 16 (15%) | 17 (20%) |
| s_l_e | |||||
| FALSE | 199 (99%) | 124 (91%) | 67 (93%) | 96 (90%) | 82 (96%) |
| TRUE | 2 (1.0%) | 13 (9.5%) | 5 (6.9%) | 11 (10%) | 3 (3.5%) |
| 1 n (%) | |||||
table_flip_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "SUPER")
| Characteristic | AFR N = 2011 |
AMR N = 1371 |
EAS N = 721 |
EUR N = 1071 |
SAS N = 851 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 190 (95%) | 108 (79%) | 59 (82%) | 81 (76%) | 72 (85%) |
| TRUE | 11 (5.5%) | 29 (21%) | 13 (18%) | 26 (24%) | 13 (15%) |
| b_l_s | |||||
| FALSE | 25 (12%) | 20 (15%) | 16 (22%) | 20 (19%) | 9 (11%) |
| TRUE | 176 (88%) | 117 (85%) | 56 (78%) | 87 (81%) | 76 (89%) |
| e_l_b | |||||
| FALSE | 14 (7.0%) | 31 (23%) | 16 (22%) | 30 (28%) | 15 (18%) |
| TRUE | 187 (93%) | 106 (77%) | 56 (78%) | 77 (72%) | 70 (82%) |
| e_l_s | |||||
| FALSE | 1 (0.5%) | 16 (12%) | 6 (8.3%) | 10 (9.3%) | 2 (2.4%) |
| TRUE | 200 (100%) | 121 (88%) | 66 (92%) | 97 (91%) | 83 (98%) |
| s_l_b | |||||
| FALSE | 178 (89%) | 119 (87%) | 56 (78%) | 89 (83%) | 76 (89%) |
| TRUE | 23 (11%) | 18 (13%) | 16 (22%) | 18 (17%) | 9 (11%) |
| s_l_e | |||||
| FALSE | 200 (100%) | 122 (89%) | 66 (92%) | 100 (93%) | 84 (99%) |
| TRUE | 1 (0.5%) | 15 (11%) | 6 (8.3%) | 7 (6.5%) | 1 (1.2%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flips, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom),], "Flips", plot_flips_noth, "SUPER", as.character(chrom))

plot_flips(df_switch_x, "Beagle", "Eagle", "pop", "X")

plot_flips(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

plot_flips(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

table_flip(df_switch_x, "pop")
| Characteristic | AFR N = 2001 |
AMR N = 2001 |
EAS N = 2001 |
EUR N = 2001 |
SAS N = 2001 |
|---|---|---|---|---|---|
| b_l_e | |||||
| FALSE | 120 (60%) | 107 (54%) | 115 (58%) | 112 (56%) | 94 (47%) |
| TRUE | 80 (40%) | 93 (47%) | 85 (43%) | 88 (44%) | 106 (53%) |
| b_l_s | |||||
| FALSE | 13 (6.5%) | 29 (15%) | 41 (21%) | 21 (11%) | 26 (13%) |
| TRUE | 187 (94%) | 171 (86%) | 159 (80%) | 179 (90%) | 174 (87%) |
| e_l_b | |||||
| FALSE | 86 (43%) | 105 (53%) | 93 (47%) | 95 (48%) | 114 (57%) |
| TRUE | 114 (57%) | 95 (48%) | 107 (54%) | 105 (53%) | 86 (43%) |
| e_l_s | |||||
| FALSE | 14 (7.0%) | 30 (15%) | 55 (28%) | 37 (19%) | 42 (21%) |
| TRUE | 186 (93%) | 170 (85%) | 145 (73%) | 163 (82%) | 158 (79%) |
| s_l_b | |||||
| FALSE | 191 (96%) | 174 (87%) | 163 (82%) | 180 (90%) | 177 (89%) |
| TRUE | 9 (4.5%) | 26 (13%) | 37 (19%) | 20 (10%) | 23 (12%) |
| s_l_e | |||||
| FALSE | 188 (94%) | 171 (86%) | 151 (76%) | 167 (84%) | 160 (80%) |
| TRUE | 12 (6.0%) | 29 (15%) | 49 (25%) | 33 (17%) | 40 (20%) |
| 1 n (%) | |||||
cross_meth_plot(df_switch_x, "Flips", plot_flips, "pop", "X")

plot_flip_rate <- function(df, m1, m2, pop, chrom = 15){
p <- df %>%
mutate(Beagle = n_flip_beagle / n_hets,
Eagle = n_flip_eagle / n_hets,
SHAPEIT = n_flip_shapeit / n_hets) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Flip rate", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
plot_flip_rate_noth <- function(df, m1, m2, pop, chrom = 15){
p <- df %>%
mutate(Beagle = n_flip_b / n_het,
Eagle = n_flip_e / n_het,
SHAPEIT = n_flip_s / n_het) %>%
ggplot(aes(x = !! sym(m1), y = !! sym(m2), colour = !! sym(pop))) +
geom_point() +
geom_abline(slope = 1, intercept = 0) +
ggtitle("Flip rate", paste0("Chromosome ", chrom)) +
theme_classic() +
xlab(m1) +
ylab(m2) +
labs(color="Population") +
scale_color_manual(values = cbPalette)
return(p)
}
chrom <- 1
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 2
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 3
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 4
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 5
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 6
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 7
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 8
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 9
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 10
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 11
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 12
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 13
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 14
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 15
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 16
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 17
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 18
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 19
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 20
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
chrom <- 21
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

| Version | Author | Date |
|---|---|---|
| 9548985 | theandyb | 2025-07-14 |
plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

chrom <- 22
plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "Eagle", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Beagle", "SHAPEIT", "SUPER", chrom)

plot_flip_rate(df_switch_trio[[chrom]], "SHAPEIT", "Eagle", "SUPER", chrom)

plot_flip_rate_noth(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "SHAPEIT", "Eagle", "SUPER", chrom)

cross_meth_plot(df_switch_trio[[chrom]], "Flips", plot_flip_rate, "SUPER", as.character(chrom))

cross_meth_plot(df_switch_trio_noth[which(df_switch_trio_noth$chrom == chrom), ], "Flips", plot_flip_rate_noth, "SUPER", as.character(chrom))

plot_flip_rate(df_switch_x, "Beagle", "Eagle", "pop", "X")

plot_flip_rate(df_switch_x, "Beagle", "SHAPEIT", "pop", "X")

plot_flip_rate(df_switch_x, "SHAPEIT", "Eagle", "pop", "X")

cross_meth_plot(df_switch_x, "Flips", plot_flip_rate, "pop", "X")

sessionInfo()
R version 4.5.1 (2025-06-13)
Platform: x86_64-pc-linux-gnu
Running under: Ubuntu 20.04.6 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/liblapack.so.3; LAPACK version 3.9.0
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
time zone: America/New_York
tzcode source: system (glibc)
attached base packages:
[1] grid stats graphics grDevices utils datasets methods
[8] base
other attached packages:
[1] gridExtra_2.3 gtsummary_2.1.0 yaml_2.3.10 reactable_0.4.4
[5] pander_0.6.6 lubridate_1.9.4 forcats_1.0.0 stringr_1.5.1
[9] dplyr_1.1.4 purrr_1.0.4 readr_2.1.5 tidyr_1.3.1
[13] tibble_3.2.1 ggplot2_3.5.2 tidyverse_2.0.0 workflowr_1.7.1
loaded via a namespace (and not attached):
[1] Rdpack_2.6.3 sandwich_3.1-1 rlang_1.1.5
[4] magrittr_2.0.3 git2r_0.33.0 multcomp_1.4-28
[7] compiler_4.5.1 getPass_0.2-4 callr_3.7.6
[10] vctrs_0.6.5 pkgconfig_2.0.3 crayon_1.5.3
[13] fastmap_1.2.0 backports_1.5.0 labeling_0.4.3
[16] utf8_1.2.4 promises_1.3.2 rmarkdown_2.29
[19] markdown_2.0 tzdb_0.5.0 ps_1.9.0
[22] nloptr_2.2.1 bit_4.6.0 xfun_0.52
[25] cachem_1.1.0 litedown_0.7 jsonlite_1.9.1
[28] later_1.4.1 broom_1.0.7 parallel_4.5.1
[31] R6_2.6.1 bslib_0.9.0 stringi_1.8.4
[34] RColorBrewer_1.1-3 boot_1.3-31 jquerylib_0.1.4
[37] numDeriv_2016.8-1.1 estimability_1.5.1 Rcpp_1.0.14
[40] knitr_1.50 zoo_1.8-13 httpuv_1.6.15
[43] Matrix_1.7-3 splines_4.5.1 timechange_0.3.0
[46] tidyselect_1.2.1 rstudioapi_0.17.1 codetools_0.2-20
[49] processx_3.8.6 lattice_0.22-6 lmerTest_3.1-3
[52] withr_3.0.2 coda_0.19-4.1 evaluate_1.0.3
[55] archive_1.1.12 survival_3.8-3 xml2_1.3.8
[58] pillar_1.10.1 whisker_0.4.1 reformulas_0.4.1
[61] generics_0.1.3 vroom_1.6.5 rprojroot_2.0.4
[64] hms_1.1.3 commonmark_1.9.5 munsell_0.5.1
[67] scales_1.3.0 minqa_1.2.8 xtable_1.8-4
[70] glue_1.8.0 emmeans_1.11.0 tools_4.5.1
[73] lme4_1.1-36 fs_1.6.5 mvtnorm_1.3-3
[76] cowplot_1.1.3 rbibutils_2.3 crosstalk_1.2.1
[79] cards_0.5.1 colorspace_2.1-1 nlme_3.1-167
[82] cli_3.6.4 gt_0.11.1 gtable_0.3.6
[85] reactR_0.6.1 sass_0.4.10 digest_0.6.37
[88] pbkrtest_0.5.3 TH.data_1.1-3 htmlwidgets_1.6.4
[91] farver_2.1.2 htmltools_0.5.8.1 lifecycle_1.0.4
[94] httr_1.4.7 bit64_4.6.0-1 MASS_7.3-65